Jonathan Archer

Jonathan Archer was a 22nd century Human Starfleet officer and captain of the, United Earth's first full-fledged starship. In that role, he was responsible for greatly expanding United Earth's presence in the Alpha and Beta Quadrants and making First Contact with more than a dozen species, among them Klingons, Andorians, and Xindi.

Considered by historian John Gill, as the "greatest explorer of the 22nd century," Archer is widely credited with saving Earth from the Xindi and paving the way for the founding of the United Federation of Planets. He would go on to become one of the Federation's earliest presidents. 

Early life
Jonathan Archer was born in 2112 to Henry Archer, the renowned warp scientist, and his wife Sally. Despite being born in upstate New York, Jonathan variously claimed to have lived "all" or "most" of his life prior to 2151 in San Francisco. 

One of Jonathan's earliest inspirations for space sciences was a copy of The Cosmos A to Z, which he got on his eighth birthday in 2120 from his father. Jonathan spent hours staring at its front cover depicting the Arachnid Nebula. Jonathan's fascination for space led to him wanting to serve in what would become the Earth Starfleet from an early age, so, in at least one astronomy book he owned as a child, he styled his name on the ex libris as "Admiral Jonny Archer". Also in his youth, Jonathan achieved the rank of Eagle Scout in the Boy Scouts. During his time there, he earned 26 merit badges, including a Wilderness merit badge which he received in a rain forest in New Zealand. In school, Jonathan was called to the principal's office only once, for passing notes to Katy Bentley. 

Tragically, in 2124, his father died of Clarke's Disease after suffering from frequent hallucinations and pain for years, sometimes not even recognizing his own son. However, the relationship that Jonathan shared with Henry's friend, Emory Erickson, strengthened, and Emory became like a surrogate father to him. 

As an undergraduate in California, he was an accomplished athlete in the sport of water polo. During his senior year, he participated in the 2134 North American Water Polo Regionals. The match featured a come-from-behind victory for his team, who were down by two goals in the last minute of play. The nature of the rally became a mantra that Archer carried forward into later life, such that he always believed he could win, no matter the odds. Following the victory in the regionals, he and his team went on to participate in the championship round of the tournament that year. 

During his early 20s, Archer was on a trip to East Africa where he witnessed a gazelle giving birth. He would remember his surprise seeing how fast the newborn managed to stand up on its feet and run along with the herd. 

A few years before Starfleet was chartered, Jonathan gave serious thought to serving on a cargo ship, but decided against it. 

Early Starfleet career
As a commander, Archer was one of four test pilots in the NX Program in the 2140s. In 2143, he and A.G. Robinson became not-so-friendly rivals in wanting to be the first to fly the NX-Alpha. Ultimately, Commodore Maxwell Forrest gave the assignment to Robinson, though Archer had spent the most time in the flight simulations and got the engines to a 92% efficiency. Robinson, however, was determined to break warp 2. He did, with Archer serving as the flight director in NX Control, but the NX-Alpha was destroyed; Robinson managed to get out just in time via an escape pod. Later, Archer, Robinson, and Lieutenant Charles Tucker III achieved warp 2.5 with the NX-Beta after modifying the engines. 

A few years prior to the launch of the Enterprise NX-01, Archer was a guest aboard the Vulcan ship, the Yarahla, which made a run to a dark matter nebula. He helped set up the graviton telescope, and also spacewalked in a Vulcan EV suit. 

Later in the 2140s, Archer was on Titan as part of the Omega training mission along with Tucker. When Tucker's environmental suit malfunctioned, Archer saved Tucker's life by preventing him from taking off his helmet on Titan's surface. 

In 2150, the final selection for the captaincy of the took place between the Captains A.G. Robinson and Archer. Admiral Maxwell Forrest gave the post to the latter, although Captain Gardner was originally considered the most suitable choice by Ambassador Soval. Archer's quarters aboard Enterprise were located on E Deck. 

First mission


Jonathan Archer's mission as captain of Enterprise began in 2151 when a Klingon officer named Klaang was attacked on Earth by the Suliban who, under the leadership of Silik, were trying to start a Klingon civil war as part of the Temporal Cold War. Enterprise's historic launch coincided with the Klingon incident and Vulcan Ambassador Soval believed the launch should be pushed off until the matter with the Klingons was resolved. Archer was not happy about the prospects of waiting around once again to launch the much anticipated warp five project and in fact believed that the Vulcan's suggestion to delay the launch was just another way to prevent humans from finally exploring space and embarking on this historic journey. Not wanting any further delays or interferences by the Vulcans, he suggested taking Klaang back to Qo'noS himself. Despite the Vulcan's objections, who believed that Humans were too volatile and provincial to take on such a matter, Admiral Maxwell Forrest fully supported Archer's proposal. He was given three days to assemble his crew and begin the mission. 

Archer recruited the Denobulan physician Doctor Phlox as the ship's chief medical officer, Commander Charles "Trip" Tucker as chief engineer and Lieutenant Malcolm Reed was assigned as the ship's armory officer. For the position of communications officer he traveled to Brazil to recruit Hoshi Sato who was an exo-linguist and had a special aptitude with alien languages. It was not easy getting Sato, who was teaching at the time, on board but the prospects of being the first human to decipher the Klingon language was very tempting. Finally, as a concession to the Vulcans, and to have access to their star-charts, Archer had to agree to have a Vulcan science officer with the name of T'Pol on board. It was expected that her assignment was temporary and that she would leave after the Klingon was returned to his home world. T'Pol herself looked forward to the end of her assignment on board Enterprise.

Even though half-way through it looked like the mission was not going to be accomplished, Archer was known for finishing what he had started. Moreover, he did not believe giving up and returning home as that would have meant failure in the eyes of the Vulcans and reaffirmation of their long-held beliefs that Humans were not ready for space exploration and should never have embarked on such a "foolish mission." After Klaang was returned to Qo'nos and war averted, Archer got word from Starfleet to "keep going" instead of returning back to Earth. Realizing that the mission would have failed without T'Pol's help, he offered to have her on board as his science officer and second in command. He admitted that ever since he could remember he saw Vulcans as an obstacle that was keeping Humans from standing on their own two feet. However, having been given the opportunity to finally begin the journey, he realized that he had to leave misgivings about Vulcans behind. T'Pol accepted his offer and made the request to her superiors personally.

Remembering his father and the dream he had, Archer gave the orders for Enterprise to finally set sail into the unknown. 

Year one: into the unknown
Archer and Enterprise made first contact with the Andorians at the Vulcan monastery at P'Jem. Even though the Andorians were initially suspicious of Humans because of their alliance with the Vulcans, they gained some measure of trust, particularly in Archer, when he assisted them in exposing the Vulcan sensor post hidden on P'Jem. Even though the decision resulted in the destruction of the ancient monastery, it was the beginning of a close relationship with the Andorians, in particular Shran, which would later prove invaluable when the Andorians came to the assistance of Enterprise during the Xindi mission in the Delphic Expanse. 

Archer's next venture concerned the discovery of a pre-industrial civilization populated by the Akaali. A plague was ravaging the planet, and a woman named Riann, a pharmacist, was trying to determine the cause. Archer helped her, and found that a hidden antimatter emitter in a local shop owned by a man named Garos had contaminated the water supply. Garos was really an alien who was mining the resources of the planet. Archer exposed him, and when Enterprise disabled his ship, Garos was forced to leave. Archer had come close to Riann during the events and became briefly romantically involved. 

Archer again encountered Silik when Silik, in the disguise of a pilgrim invited on Enterprise, tried to disable the ship. He also met Daniels, who he thought was a crewmember, but was in reality a temporal agent from the future. Daniels informed Archer that Silik was trying to change the future, but Silik denied this and said it was Daniels who was the culprit. When Silik was found in engineering and confronted, he escaped; it was apparent he was the saboteur. 

Archer helped rescue a Klingon ship that was losing orbit and falling into a gas giant. Bu'kaH, a survivor of the accident, was convinced to cooperate with Archer in a rescue attempt after he convinced her that she would be letting her crew die a dishonorable death. Bu'kaH reluctantly let Archer take her on the reinforced shuttlepod toward her ship, along with an antidote to the neurotoxin. The Klingon crew was rescued along with Hoshi Sato, T'Pol, and Malcolm Reed, who were marooned on the ship in a previous rescue attempt. 

Archer and T'Pol were captured on an away mission on Coridan by rebels backed by the Andorians against the government supported by the Vulcans. Shran, along with Reed and Charles Tucker III, rescued them. 

Archer visited a planet where Eska engaged in hunting sentient beings, telepathic shapeshifters. When they were afraid, they emitted a chemical that gave away their location and made them easy targets. On Archer's orders, Phlox came up with a plan to mask the chemical, which shielded them from the hunter's scans. The hunters left when they could no longer use their scans, and the beings were safe. 

Archer made first contact with the Ferengi later that year, although the aliens in question would remain anonymous; official first contact was eventually made by Jean-Luc Picard. The Ferengi captured Enterprise by rendering the crew unconscious, robbing the ship of all valuables. When Archer woke, he, along with Tucker and T'Pol, was able to play the Ferengi off against each other and retake the ship. 

Archer accompanied a landing party down to a barren planet to salvage an abandoned ship. They had been told by D'Marr, an alien they met, about the ship and also that it was haunted. Arriving on the planet, the party found that a group of Kantare had inhabited the planet. Their behavior seemed strange, though, especially when Archer offered to transport them back to their homeworld. They learned that all but two of the Kantare were holograms created by Ezral, who blamed himself for the crash and the death of his friends. He had created the holograms to keep his daughter, Liana, company. Enterprise returned both to their homeworld. 

Archer, along with Travis Mayweather, was imprisoned in a Tandaran prison camp. The Tandarans were at war against the Suliban Cabal, and had interned innocent Suliban in the camp. Archer learned of the plight of innocent Suliban, who weren't involved with the Cabal but still suffered the wrath of the Tandarans by being imprisoned for years in these horrid camps. Archer and Mayweather, along with Enterprise, escaped and released the Suliban. 

Archer was captured by a symbiotic creature who had stowed away on Enterprise. The creature assimilated Archer's nervous system, along with others it had captured. When Enterprise offered to take it back to its home so it could be attached to its large host, it released Archer and the others. 

During a visit to Zobral's village, Archer and Tucker got caught up in a civil war, and after an attack, they became stranded in a vast desert. With Zobral's help, Enterprise rescued them. 

While on shore leave on Risa, Archer met a Tandaran named Keyla, who, in the disguise of a Human, tried to obtain information about the Suliban from him. 

In March of 2152, after it appeared his ship's mission was over because of the destruction of the mining colony on Paraagan II, Archer was transported to April 9, 2151 by Daniels, who revealed the Suliban were responsible for what had happened. Returning to the present, Archer used knowledge given to him by Daniels, including the technical skill to construct a quantum beacon, to board a Suliban stealth-cruiser and prove what they had done. As a result, Silik demanded Archer. To save Archer, Daniels transported him to the 31st century, causing a major disruption in the timeline that apparently destroyed Earth. Fortunately, Archer and Daniels were able to repair the timeline, though not before Archer managed to learn that he was vital to the creation of the future United Federation of Planets. 

Year two: first contact
Archer made a regrettable first contact with the Romulan Star Empire. When Reed tried to disarm a mine attached to the hull, a spike thrust out of the mine and through Reed's leg, pinning him to the ship's hull. Archer, with Reed's instructions, was able to disarm the mine and save Reed. This led to a stop at an automated repair station that was just as dangerous as the minefield. The station used humanoid brains as coprocessors in its computer by physically connecting the captive's nervous system to its network. The crew escaped, but not before Mayweather became one of the station's adjuncts and had to be saved. 

After insulting the Kreetassans during an away mission, Archer's dog, Porthos, was infected with a deadly disease. Phlox cured him, but not before Archer spent a whole night worrying about the relations with the Kreetassans and comforting his dog. Phlox not only saved Porthos, but provided Archer with advice that solved the diplomatic problem. 

Archer led a team of crewmen in teaching a mining colony to defend itself against Klingons. They stayed with the miners while they drove off the Klingons. 

Archer helped T'Pol track down Menos, a rogue Vulcan agent who had become a weapons smuggler. When Menos played on T'Pol's guilt concerning an earlier incident in capturing another rogue agent, Archer was able to help her put her guilt aside and do the right thing. Archer and Reed were sentenced to death when exploring a planet. Reed had accidentally left behind a communicator, and when he and Archer tried to retrieve it, they were captured. Their captors believed they were super-soldiers sent by their enemies. Heeding T'Pol's long-offered advice on inter-species contact, Archer decided that he and Reed would have to be hanged in order to avoid contaminating the pre-warp civilization. This early, solemn consequence of the as-yet-uncodified Prime Directive was averted, however, when the crew of Enterprise saved Archer and Reed using a captured cloaked Suliban cell ship. 

Later that year, Archer granted asylum to Takret refugees. During a radiation storm, they had to take refuge in the catwalk. The military, pursuing the refugees, boarded Enterprise and almost destroyed it when they tried to start the warp engines. 

Enterprise investigated a black hole that was part of a trinary star system. However, the radiation from the trinary system affected the crew, causing odd behavior and rendering them comatose. The exposure would have killed them, but T'Pol awakened Archer, who was able to pilot the ship away from danger. 

Archer was once again drawn into a dispute between Vulcans and Andorians. He avoided a war when he mediated a territorial dispute between the two species. 

Archer and Tucker were arrested and sentenced to Canamar for false crimes. A fellow prisoner was able to hijack the ship with their help, but when they found out the prisoner was going to beam off the ship and crash it, killing the rest of the prisoners and guard, they foiled his plot and were rescued by Enterprise. 

When Enterprise discovered a futuristic vessel adrift in space, Archer ordered it brought on-board for further investigation, and a Human body was found in the ship. The Suliban and the Tholians claimed that the ship belonged to them, and demanded that Archer turn it over immediately. Archer was worried that the course of the Temporal Cold War could be affected. During the battle, as they tried to activate the ship, it vanished, and the Suliban and Tholians left. 

Archer and his crew fought against the Borg two centuries before the USS Enterprise (NCC-1701-D)'s encounter with them. Two Borg drones had been found in Earth's Arctic Circle and thawed out by a team of scientists that they then assimilated. These drones were from the unsuccessful attempt by the Borg in the 24th century to stop the flight of Earth's first warp-capable vessel via time travel. The drones, old and new, left Earth on the scientists' assimilated arctic transport. Enterprise intercepted and destroyed the ship, with Archer and Reed boarding it and setting explosives to make this possible. In the course of doing this, they fought and killed several of the drones. 

During first contact with the Vissians, Archer became close with their captain, Drennik. Drennik invited Archer to join him when he took the Vissian strato-pod deep into the hyper-giant. This first contact would end tragically, when Tucker interfered with a cogenitor, a third gender of the Vissians who were second-class citizens. Archer was asked by the cogenitor to grant asylum, which he denied after a meeting with the Vissians. Drennik contacted Archer and told him that the cogenitor had committed suicide. 

After the Broken Bow incident, Archer had many other dealings with the Klingons.

In late 2152, Archer was captured by the Klingons after assisting Raatooras rebels. Put on trial on Narendra III, he was spared the death sentence through the efforts of his lawyer, Kolos. Archer was sentenced to labor in the dilithium mines on Rura Penthe, but managed to escape. He was hunted by the Klingons for this offense, at first through bounty hunters such as the Tellarite Skalaar, resulting indirectly in Archer making Human first contact with the Tellarites. Skalaar believed that the Klingons would return his ship to him, but when he found out that they scrapped it, he helped Archer escape. 

During the expedition to the Delphic Expanse, Archer was hunted by Duras, who had been dishonored when Archer saved the Raatooras rebels from him. Archer destroyed Duras' ship and its crew with it. 

Year three: the Xindi attack
After the Xindi probe attack on Earth in 2153, Archer was given a new mission: search for the Xindi superweapon, which required entering a dangerous region of space known as the Delphic Expanse, in order to find the ones responsible for the attack and prevent them from launching their superweapon to destroy Earth. It took nearly six weeks before Enterprise came into contact with an actual Xindi, and even then he proved to be of little help, directing Archer to coordinates that contained nothing but a field of debris which used to be the planet Xindus. 

In September of 2153, while investigating an abandoned Xindi vessel on a planet, Archer, Hoshi Sato, and Malcolm Reed succumbed to a virus that mutated them into Loque'eque, a primal lifeform. Tret, the leader of an alien race, attempted to kill Archer in order to eradicate the virus. Even after being cured by Phlox, Archer continued to suffer strange dreams of the Loque'eque city. Phlox kept a sample of the virus as per Archer's instructions, as destroying it would effectively make the Loque'eque completely extinct. 

While visiting a planet to obtain trellium-D, a substance that would protect Enterprise from the anomalies of the Expanse, Archer helped rescue a woman, Rajiin, from slavers. However, Rajiin was really an agent of the Xindi sent to obtain information about the Humans. Thus, the first battle between Enterprise and the Xindi occurred. The Xindi-Reptilians boarded the ship and took Rajiin so that they could get the information she obtained. 

Enterprise encountered a Vulcan ship in the Expanse. When Archer and T'Pol boarded the ship to see if there were survivors, they found that the crew had gone insane. The Vulcans were intent on killing them and, after they escaped, Archer's only choice was to destroy the ship. 

Archer spied on a Xindi research facility, and convinced a Xindi-Arboreal, Gralik, that the Humans were not a threat. Gralik gave Archer a canister of kemocite, fuel for the superweapon, to analyze. 

In October of 2153, Archer suffered a mild concussion from an encounter with a spatial anomaly. He eventually recovered. 

Archer encountered a Human colony populated by descendants of 19th century Americans. He helped them reconcile with the Skagarans, who had originally kidnapped them from Earth to work as slaves on their planet. The descendants of the Humans revolted and took over the planet, relegating the Skagarans to slaves. Archer helped convince the sheriff and town leader, MacReady, to make changes, but only after a gunfight with some local cowboys. When the Humans expressed a desire to be reconnected with Earth, he was forced to explain that his ship could not accommodate them. Nevertheless, he promised that Starfleet would eventually recover them. As a stopgap measure, he at least provided them with the current history of Earth so that they could better prepare themselves for better reintegration with the main human population. 

Archer and T'Pol went back in time with the help of Daniels to stop the Xindi from producing a bioweapon that would destroy Earth in the past. He killed the Xindi and returned to the present. 

Archer dealt with a group of religious zealots who hijacked Enterprise, planning to use it in a religious war. When the lead zealot demanded that a crewmember be put to death for the 'blasphemy' of taking scans of the "sacred realms", Archer tricked them into using the transporter on him; allegedly, it would disperse his atoms, but really he was just teleported to another part of the ship. After the ship was retaken, he returned the zealots to their homeworld, where he revealed that their planet had been practically destroyed already, asking them before he left to consider if the "truth" really was that important. 

An Andorian starship, led by Shran, helped Archer and Enterprise track down the Xindi superweapon by following a signal from on one of the kemocite canisters that Archer had planted when he visited a research facility earlier in the year. The Andorians captured the prototype of the weapon, but Shran was under orders to return it to Andoria. Before Shran could leave with the weapon, Archer activated it, and Shran was forced to jettison it before it exploded. Despite the conflict, Shran transmitted details of the weapon to Archer. 

In an attempt to gather the whereabouts of the superweapon, Archer captured Degra and, using mind control, attempted to convince him that both have been in a Xindi prison. He tried to gain Degra's trust so that Degra would give them the location of the weapon. Archer told Degra that the weapon had been used and Earth had been destroyed, but that a civil war had broken out on Xindi, resulting in a great loss of life. Degra discovered the ruse, but not before he let slip that the weapon was on Azati Prime. 

On the way to Azati Prime, Enterprise discovered a damaged Xindi-Insectoid vessel with no life signs on board. Archer discovered a hatchery containing Xindi eggs, some of which were still viable. He was suddenly spattered by a strange liquid that spewed from one of the egg sacs, and Phlox determined that Archer was hit by a mild neurotoxin that made him believe that he was the eggs' caretaker, and his actions began to jeopardize their mission. 

On the way to Azati Prime, Enterprise found a damaged ship containing an injured alien. It was determined that the alien was a test subject and that his people from another dimension would take over the quadrant when Earth was destroyed. They were the Sphere Builders, who had been manipulating certain Xindi species into destroying Earth. 

Arriving at Azati Prime, a fierce firefight began. Archer discovered that the weapon was hidden in an ocean. At that point, he declared he was not going to order any more deaths, instead choosing to personally destroy the Xindi superweapon, despite attempts by T'Pol and Daniels to talk him out of it. However, the Xindi intercepted and captured him, though they released him after a lengthy interrogation. Degra was beginning to believe that there were aliens behind the war. 

In February 2154, Archer went before the Xindi Council to convince them to not launch the Xindi superweapon at Earth. He had a hard time, but quickly made an ally of Degra. The other Xindi-Primate councilor, Jannar, and Kiaphet Amman'sor soon came around to Archer's side as well, but Commander Dolim betrayed the Council, stole the weapon, and killed Degra. 

In the final battle to save Earth, Enterprise was joined by the Xindi-Aquatics and Xindi-Primates. As the fleet of Reptilian and Insectoid ships were destroyed, the Sphere Builders, the aliens behind the plot, tried to intervene. Sato was captured by Dolim to decode the weapon's software so it could be activated. The MACOs, under the leadership of Major J. Hayes, rescued her, but Hayes was killed. Archer, along with Reed and the MACOs, used Degra's ship to intercept the superweapon. Enterprise proceeded to destroy the spheres in the Expanse. Boarding the superweapon, Archer, with Sato's help, was able to cause a reversal overload that would destroy the weapon. As the away team beamed out, Archer was left behind and confronted Dolim, whom he killed. Enterprise destroyed all the spheres and ended the alien interference. Archer was believed to have been killed, having been aboard the Xindi superweapon as it exploded while approaching Earth. 

After the destruction of the Xindi superweapon, Archer was saved when he was thrown back in time to World War II. He found that as part of the Temporal Cold War, the Na'kuhl were helping the Nazis win the war by conquering America. Archer was able to destroy the time conduit and end the war. 

Year four: making friends...and enemies
Several months after returning to Earth with Enterprise, Archer was sent on a mission to stop a group of rogue Augments, relics of the Eugenics Wars that had been resurrected by Dr. Arik Soong. They had attacked and stolen a Klingon ship, and the Klingons threatened war unless the Augments were brought to justice. Archer, along with Soong, tried to find them. Soong escaped and joined the Augments, and Archer found them at Cold Station 12, a Starfleet facility where other Augment embryos were stored. He was captured and left to die when the Augments triggered a self-destruct procedure. Archer disarmed the self-destruct, and was able to defeat the Augments, recapture Soong, and preserve the peace with the Klingons. 

Earth's embassy on Vulcan was bombed, resulting in the death of Archer's friend and mentor, Admiral Maxwell Forrest. Although a Vulcan splinter group, the Syrrannites, was blamed, Ambassador Soval urged Archer to travel to their hideout in Vulcan's Forge and find the truth. Accompanied by T'Pol, he met their leader, Syrran, there. Syrran was secretly carrying the katra of Surak, and prior to his death by wounds from a desert storm, he transferred Surak's katra to Archer. Archer, guided by Surak's katra, met with the remaining Syrrannites led by Syrran's lieutenant, T'Pau, and found the long-lost Kir'Shara, a record of Surak's original teachings.

Archer and T'Pau headed to the Vulcan capital to confront the Vulcan High Command. It was discovered by Soval, Trip Tucker, and Malcolm Reed that the bombing was the work of V'Las, the leader of the Vulcan High Command who wished to wipe out the religious group and start a war of conquest against Andoria. Archer and T'Pau, after presenting the Kir'Shara, averted a war between Vulcan and Andoria. In the process, the Vulcan High Command was dissolved, beginning a new era in the development of Vulcan society. No longer would the Vulcans hold back Humanity's advancement into space; for Archer, it was a life-long dream fulfilled. The event was mutually beneficial: Vulcan society reverted to the more altruistic and logical path Surak had originally intended, and Archer gained a greater insight into Vulcans than ever before as a result of having carried the katra of Surak. 

Archer would later make First Contact with the Organians, though his memories of the event were completely erased. He then become embroiled in high-level galactic intrigue when he rescued Commander Shran from the destruction of the Kumari, which Shran blamed on the Tellarites. However, Archer discovered that it was truly the Romulan Star Empire that was trying to destabilize the entire region through the manipulation of other galactic powers into fighting one another using a Romulan drone-ship. Discovering the ruse, he organized a landmark combined fleet effort of Humans, Vulcans, Andorians, and Tellarites to search for the Romulan vessel, beginning the first steps in uniting these disparate races against a common enemy. 

Archer again came into conflict with the Klingons during their Augment crisis. The Klingons used Human Augment DNA in their attempts to genetically engineer their own Augments, unleashing a virus that threatened the Klingon race with extinction. They kidnapped Phlox so that he could help find a cure. Archer was able to rescue Phlox, but not before he helped him find a cure for the virus. 

Archer foiled the plot of John Frederick Paxton, the leader of Terra Prime, a xenophobic terrorist group, who threatened to attack all alien ships and Starfleet Command with weapons stationed on Mars. He was able to deactivate the weapon and arrest Paxton. Afterward, he was influential in restarting negotiations for the formation of a Coalition of Planets, giving a speech which persuaded delegates from various alien worlds to continue the steps towards an alliance with Earth. 

Later career
Archer's command of Enterprise ended in 2161, after which he signed the charter ratifying the Coalition of Planets, which would ultimately lead to the formation of the United Federation of Planets.

After the founding of the Federation, Archer went on to serve in the Federation Starfleet. At his retirement from Starfleet, he was Chief of Staff at Starfleet Command with the rank of admiral. Archer became an honorary member of the Andorian Imperial Guard in 2164, Federation ambassador to Andoria in 2169, a representative on the Federation Council in 2175, and ultimately President of the United Federation of Planets in 2184, where he served for eight years. 

Moral conflicts
As one of the first Starfleet captains to explore the galaxy, Archer was sometimes faced with moral decisions. Consequently, he was at times forced to bend the morals to which he once strictly adhered, especially during his time in the Delphic Expanse, though he told T'Pol he could not save Humanity if he lost what made him Human. 

During their first year in space, the Enterprise visited the Valakians, who were being killed off by an unknown epidemic; they would be extinct in less than two centuries. The other species on the planet, the Menk, who were a second-class species, were unaffected. Archer wanted to know if a cure was possible. Phlox told him that he had found a cure, but what was happening was natural evolution and that the Menk showed evidence of an awakening and had the potential to become the dominant species on the planet, which wouldn't happen as long as the Valakians were around. Archer's decision to withhold a cure and let nature take its course was against all his principles, but he realized that he had no right to interfere in another culture and play God; this could be used as an example of an early Prime Directive. 

Enterprise was ordered to evacuate a group of Denobulan geologists from Xantoras, a world that had been taken over by the military. One of the evacuees was an Antaran named Hudak. Hudak was dying, but refused to be treated by Phlox, because the Antarans and the Denobulans were mortal enemies. Phlox wouldn't treat a patient against their wishes even when Archer threatened to order Phlox to do so. Archer could not understand Phlox's attitude, but honored his wishes. Phlox was able to convince Hudak to be treated. 

When the Vissians informed him that their cogenitor had committed suicide due, in part, to Commander Tucker's actions, Archer told Tucker that he wasn't in the position to judge the rightness of the Vissian culture and that he hoped Trip had learned his lesson about interfering in other cultures. 

Archer once went so far as to torture an Osaarian pirate named Orgoth in order to find his ship that had stolen weapons, food, and precious supplies. 

Archer authorized Phlox to create a clone of Trip Tucker, Sim, so its neural tissues could be used to save Tucker, who was hurt in an accident and was dying. This transplant would have ended Sim's life. Phlox refused to perform the operation until Sim agreed to it. 

Archer ordered the destruction of a Xindi monitoring station which would reveal the Enterprise's position, killing three Xindi in the process. 

Archer was so obsessed with accomplishing the Xindi mission that he stole a warp coil from an Illyrian vessel; Enterprise needed the warp coil to be able to stop the Xindi superweapon that would destroy Earth. The theft left the Illyrian vessel with three years added onto its voyage home. Though he did leave them trellium, food, and supplies, Archer couldn't help but come into a conflict with what he believed was right and wrong. 

Henry Archer
As a boy, Jonathan often built model spaceships with his father. The two also spent time together flying the models.

On Jonathan's eighth birthday, his father gave him his first astronomy book, The Cosmos A to Z. Archer spent hours staring at the cover of this book, which featured an image of the Arachnid Nebula. Shortly thereafter, his father gave him a tour of the Warp Five Complex. 

Sadly, Henry Archer died from Clarke's Disease when Jonathan was 12, leaving his mother to raise him. During the last two years of his life, Henry had difficulty recognizing Jonathan or his mother as a result of the disease. 

Sally Archer
Often, when Jonathan had trouble sleeping as a child, he would ask his mother recite a poem for him. One poem he frequently requested from her was "The Song of the Wandering Angus." While listening, Jonathan imagined how the woman in the poem would appear, creating her image in his mind. He did not learn until years later that the poem was written by William Butler Yeats. 

Charles "Trip" Tucker III
Archer met Charles Tucker III, or "Trip", during the NX Project. Archer was a pilot and Tucker was a lieutenant on Captain Jefferies' engineering team. After the NX-Alpha was destroyed and the project was going to be canceled, Tucker and Archer teamed up with Commander A.G. Robinson to save the program. They launched the NX-Beta without permission, and were ultimately successful. 

Archer and Tucker's friendship continued to grow when both were assigned to the Australian Outback for survival training. Archer saved Tucker's life on a number of occasions. On Titan in 2147, Tucker's EV pack froze up and he got nitrogen narcosis. Archer stopped him when he tried to remove his helmet. Archer later saved a delirious Tucker from heatstroke when they were stranded on a desert planet. 

On Enterprise, Tucker became Archer's right arm. They had their meals together and shared many interests. Archer never got tired of listening to Tucker's Southern home-spun stories. Tucker, for his part, knew how to relieve Archer's stress. When Archer was upset about a first contact with the Kreetassans, Tucker gave him a data module of the Stanford versus Texas water polo match. 

No matter what kind of a jam he was in, Archer always knew he could count on Tucker, both professionally and personally as his friend. When in 2152, Archer and Malcolm Reed - who tried to find a communicator left behind on a pre-warp alien planet - were sentenced to death, it was Tucker and his efforts that rescued them from execution by the natives. He also rescued Archer from bounty hunters who wished to turn Archer over to the Klingons. 

Archer and Tucker's relationship was not always stress-free. During first contact with a race known as the Vissians, who used a third gender called a cogenitor for reproduction, Tucker - who was upset at how it was treated, took it aside in an attempt to open its eyes. The cogenitor didn't have a name, was not allowed to leave its room or receive education. It was treated somewhat lower than a second-class citizen even, because - as Tucker pointed out - "even Porthos had a name." Tucker had the cogenitor's DNA sampled and in a side-by-side comparison, Doctor Phlox discovered that intellectually the cogenitor was on the same level as its counterparts, thus no more superior or inferior. Tucker used this as an opportunity to take on the cogenitor, teaching it how to read and telling it that it had the same rights as everyone else and that it should stand up for itself, asserting its freedom and rights as an individual. When the cogenitor asked for asylum on Enterprise and Archer denied it, it committed suicide rather then keep living as it had. Archer was both disappointed and furious that Tucker had jeopardized not only their first contact with the Vissians but also indirectly caused the death of the cogenitor. Tucker told Archer that he did exactly what Archer would do; a statement which left the captain even more upset as he himself often had to wrestle with the fine line of doing what he thinks is right and interfering with other species. Archer told Trip that it was not his place to judge the fairness of another culture and that he should never have interfered. While Tucker was shocked at how the situation had unfolded, as he never foresaw this going so far, Archer believed him to be responsible for the cogenitor's death and asked him to weigh the repercussions of his actions. Archer did not formally discipline Trip, but made it clear how disappointed he was in him for having acted so impulsively and irresponsibly. 

After the first Xindi attack on Earth in 2153, Archer was the one to break the news to the Enterprise crew. This was of particular significance to Trip as his younger sister, Elizabeth, was an architect who lived in Florida - part of the area that was destroyed by the Xindi weapon. Even though Archer did not know whether Trip's sister was among the casualties, he comforted him anyway, suggesting she may have been visiting elsewhere when the attack took place. When it turned out that his sister was among the victims killed, Trip's reaction was naturally one of anger towards the Xindi; he and Archer agreed that they would find the people responsible and hold them to account for their actions. "Whatever it takes", Archer said. 

During the Xindi mission, Tucker became seriously injured when an explosion on top of the warp core flung him to the lower engineering deck. Upon arriving in sickbay, he had lapsed into a coma due to the extensive neural damage he had sustained. Dr. Phlox insisted the only way to treat him was to use a Lyssarrian desert larvae to create a clone of Tucker and then use that to harvest the required neural tissue. Archer, aware of the moral implications, gave the order to proceed, thereby saving Tucker's life. Even though it was not an easy decision and he was aware that the clone would have to be sacrificed, Archer still bonded with him, giving him the name "Sim", as he was an exact facsimile of Trip, including all of his memories and experiences. When the time finally came, Archer held a funeral service for Sim who he said was, "one of their own". 

Later that year, Archer was infected with a Xindi-Insectoid neurotoxin causing him to act irrationally. He lost all sense of self and became obsessed with protecting a Xindi insectoid hatchery the crew had found. Archer went to great lengths to protect them, such as relieving senior officers of their duties and assigning MACO units to all decks of the ship. It was only due to Tucker's stubbornness that he became aware something was controlling the Captain's behavior and, with the help of Phlox and T'Pol, they managed to incapacitate him and cure him of the neurotoxin. 

As they grew closer to finding the Xindi weapon, Archer had managed to convince the weapon's creator, Degra, to help them in their cause. This resulted in him coming aboard Enterprise where he and Tucker came to blows over the death of Elizabeth. Tucker, out of respect for Archer, calmed down, eventually coming to realize that the whole situation wasn't Degra's fault for he was simply acting on what he had been told about Humans. The Xindi weapon finally reached Earth in February of 2154 where it was destroyed by a strike team led by Archer. Even though they were successful in their mission, Archer was believed to have been killed in the explosion. This had a noticable effect on Tucker who couldn't seem to grasp what had happened. However he didn't have much time to grieve when it soon became apparent that the ship had been transported into the 20th century, right amidst the events of World War II. Upon investigation, it was discovered that a Temporal Cold War faction was trying to alter the timeline on Earth so the allies never win the war. During an attempt to stop them, Tucker became reunited with Archer who had survived the explosion and had been transported back in time like the rest of the crew, much to Tucker's relief. Later that year, Tucker became infected with a silicon-based virus, as part of an experiment by the Organians. During his time in the decon chamber and a deteriorating health, Archer visited him periodically to check how he was. When one of the Organians revealed itself and their "experiment", it was Archer's plea that convinced the aliens to cure both Trip and Hoshi Sato. 

After a somewhat awkward courtship with T'Pol and the feelings he had developed for her, which she could not reciprocate at the moment, Trip requested a transfer to the, citing the new ship needed experienced crew. Realizing this was just an excuse, Archer asked Tucker for the real reason but Tucker did not want to reveal his true motivation for leaving. Instead, he solemnly asked that Archer grant his request as his friend, to which Archer replied, "I'm asking you to stay...as a friend". Despite this, Tucker still left Enterprise, which put somewhat of a strain on their friendship. 

Trip eventually decided to return to Enterprise permanently when he and T'Pol could no longer deny their feelings for one another. Archer and Tucker's friendship remained stable from this point on. 

In 2161, Tucker died saving the ship and crew. As he was placed into the medical imaging chamber, he gave one last smile to Archer as if to say "everything will be fine". 

T'Pol
Archer's and T'Pol's first meeting was not very pleasant for either one of them. Archer had just found out that the Vulcans wanted to delay Enterprise's much anticipated launch due to the Klingon incident and to make matters worse, T'Pol interjected, berating Archer and humanity for their volatile and provincial nature that she believed rendered them unfit for space exploration. Archer was angered and his response to her was that he was restraining himself a great deal as he really wanted to just "knock [her] on [her] ass." When she was later assigned to his ship as his first officer and science officer or as Archer called it "a chaperon", he was looking forward to her leaving after the mission was over as he found T'Pol cold, uncaring, cynical, and humorless. To make matters worse, T'Pol was not particularly fond of Archer's pet dog, Porthos whose smell bothered her. She insisted on cutting vegetables with a knife as Vulcans do not touch their food and she did not find Archer's initial attempts at humor and breaking the ice worth entertaining. In turn, Archer made it clear to her that she was not to disclose anything they discussed to her superiors on Vulcan. As the mission progressed, however, Archer and T'Pol found common ground. He was wounded saving her life in a fire-fight, and T'Pol assumed command and led Enterprise in pursuit of Suliban who had kidnapped Klaang. As the acting-captain she could have easily turned around and left but she chose to continue the mission, knowing that it was what Archer wanted. This gave him a new-found respect for her as he was surprised at the loyalty she exhibited after the initial cold reception. The mission was a success and when T'Pol was scheduled to leave Enterprise as agreed, Archer asked her to join his crew, as he no longer wanted to hold grudges and instead start freshly with the Vulcans. 

Archer began to trust T'Pol when she didn't turn a blind eye when the secret Vulcan surveillance station at P'Jem was revealed and helped Archer expose the spy station to the Andorian commandos. 

When Ambassador V'Lar came aboard Enterprise in 2152, she sensed a great bond between Archer and T'Pol, of "trust... and friendship." 

Archer lent T'Pol support when she was sent on a troubling mission for the Vulcans: She was to apprehend a former Vulcan agent who had become an arms dealer. Archer assisted her and reassured her self-doubts during the mission. The incident solidified the trust between the duo. 

T'Pol took meals in the captain's mess, and once drank wine and entertained Archer with a story of an ancestor who visited Earth before first contact. Archer convinced T'Pol to interact with the crew. She went to movie night with them, and actually liked a movie called Frankenstein. 

Archer opened up to T'Pol when his good friend and former rival, A.G. Robinson, died. T'Pol listened to Archer's story about the two of them and offered him a shoulder to lean on. 

In the end, it was T'Pol who was with Archer before he gave a speech at the signing of the Federation Charter. Overcome with emotion, T'Pol and Archer embraced before his speech. 

Increased friction between Archer and T'Pol in 2152, lead Dr. Phlox, who also had a degree in psychiatry, to believe that Archer was sexually attracted to T'Pol but was frustrated, as a romantic relationship between him and his first officer would be very inappropriate. He believed that Archer's inordinate anger towards T'Pol's opinions on him and other unexpected behavior he exhibited stemmed from Archer subconsciously knowing that his attraction to her was inappropriate. At first, Archer denied that there was any sexual attraction but after an erotic dream with T'Pol in it, he opened up to the doctor, wondering what to do. Phlox told him that simply being aware of it would be the best course of action as talking to her about it would make matters worse. In a later discussion with T'Pol, Archer told her that he would like to minimize the friction between the two of them, a type of friction which could especially develop between people of the opposite sex. T'Pol replied, matter-of-factly, that in this case it was ideal that he was her superior officer, as that way they would be in a position that would not allow them to become attracted to one another as that kind of attraction would exacerbate the very friction Archer was hoping to avoid. Archer agreed that such a relationship would be inappropriate and the possibility of a romance between the two was never explored again. 

Thy'lek Shran

 * Archer: We keep doing each other favors.


 * Shran: Isn't that how alliances are born?

Shortly after taking command of the Enterprise, Archer encountered the Andorian commander Shran. In their first confrontation, at the Vulcan monastery of P'Jem, Shran believed Archer's crew were there to help the Vulcans spy on the Andorians. While being kept hostage, Archer managed to contact Enterprise, which sent a rescue team. During a firefight inside the monastery's reliquary, one of the Vulcans accidentally destroyed a curtain, which was covering the entrance to the Vulcans' sensor array. Archer asked T'Pol to give Shran all the data she had collected, to which Shran said that he owed a debt to Archer. 

In 2152, Shran met with Enterprise crewmembers attempting to rescue Archer and T'Pol from the rebels on the planet Coridan. He told them he had "lost sleep" over the fact that he owed a favor to Archer, and so wanted to help rescue him to write off his "debt". 

Later that year, Shran insisted to Vulcan ambassador Soval that Archer be the mediator at talks between their two species, because on their previous encounters, Archer had been "objective". The Vulcans were initially annoyed at the request, due to their disdain with Humans, but eventually agreed, and the negotiations were completed successfully. 

In late 2153, Shran's ship, the Kumari, was dispatched to the Delphic Expanse to secure the prototype Xindi superweapon, to use in their conflict with the Vulcans. Shran arrived in the Expanse and aided Enterprise, claiming (under false pretenses) that the Vulcans had only spared one officer to help Enterprise during their mission. The Kumari and Enterprise were able to effect a joint mission to steal the prototype, which was stored in the Kumari's cargo bay. However, Shran then informed Archer of the Imperial Guard's plan, and gave Archer an escape pod so he could return to Enterprise. When encountering spatial anomalies, Enterprise caught up with the Kumari, and Archer told Shran that he would detonate the weapon in the Andorian ship's cargo bay if necessary. Shran thought he was bluffing, but Archer proceeded with his plan and, although jettisoned, the resulting explosion severely damaged the Kumari. Later, Shran covertly sent Archer invaluable information on the weapon. 

As the Xindi superweapon approached Earth, the Kumari provided assistance, destroying Xindi Commander Dolim's ship, telling Archer that now the Human was in his debt. 

In 2154, Shran led a group of Andorian ships attempting to stop a Vulcan fleet launching a preemptive strike against them. As the Vulcans were ordered to destroy Enterprise, Shran went to their assistance again, claiming that Archer now owed him two favors. 

The two met again in November of 2154, when the Kumari was attacked and destroyed by a Romulan drone-ship posing as a Tellarite cruiser. Shran was very bitter about the loss of his ship, and openly blamed the Tellarites. However the Romulan plot was eventually revealed by Archer, who was attempting to keep an already fragile alliance between the Andorians, Tellarites and the Vulcans. 

In 2158, Shran went into hiding. Three years later, he enlisted Archer's help in looking for his daughter, Talla, who had been abducted. The pair were able to initiate a rescue, with the help of the Enterprise's crew. 

Malcolm Reed
Early in Enterprise's mission, Archer took steps toward forging a relationship with his senior staff, including his armory officer, Malcolm Reed. During the first year of their voyage together, Archer and Hoshi Sato took great pains to learn more about Reed, even going so far as to contact members of his family to discover his likes and dislikes. While the effort culminated in a friendly birthday celebration for Reed, the relationship between Archer and Reed failed to develop substantially. 

It wasn't until a full year after the launch of Enterprise that Archer and Reed were able to plan a private breakfast in the captain's mess. While Reed mistook the meal for a more professional meeting, Archer was able to coax the armory officer into a personal, though somewhat awkward conversation. Speaking freely, Reed revealed that he felt Archer was too lax a commanding officer. These sentiments were later repeated when Archer chose to risk his own life in an attempt to save Reed when he became trapped on the hull of Enterprise during the Romulan minefield crisis. Though both men survived and some level of trust was achieved between Archer and Reed, a closer relationship failed to materialize and Reed continued to doubt Archer's resolve as an effective commander. 

In 2154, following the Xindi mission, Archer and Reed would clash when Reed's loyalty to Section 31 put him in direct conflict with Archer. Performing a minor act of sabotage against the investigation into the disappearance of Dr. Phlox, Reed was subsequently thrown into the brig. Though several heated conversations took place, Archer was able to get through to Reed and the mission ultimately proved successful. 

Phlox
Archer initially met Dr. Phlox in San Francisco upon learning of the incident involving the Klingon Klaang in Broken Bow, Oklahoma. Phlox was treating Klaang and saved his life; this impressed Archer, who recruited Phlox soon after to serve as chief medical officer aboard Enterprise. Phlox was one of only two aliens among the crew, and became one of its most valuable members. He would become one of Archer's most trusted advisers and on many occasions, his counselor. Phlox would also play devil's advocate for Archer. There were a few issues that they would come into conflict over, but this only strengthened their friendship. 

Early in the mission, Archer and Phlox argued over a cure for an epidemic on the planet Valakis, whose population had two species, the Valakians and the Menk. Phlox discovered that the illness was genetic, and that the Menk were evolving and would become the dominant species, while the Valakians would become extinct. Archer wanted to give them a cure, but Phlox believed that it was not ethical, because such a cure would interfere with nature. Archer was eventually convinced that they had no right to play God, and gained a new respect for Phlox and his counsel. 

Archer looked to Phlox for advice on how to deal with various races, since Phlox had experience in such matters. He sought advice on how to deal with the Klingon Bu'kaH, in order to persuade her to help with a rescue attempt. Archer was convinced by Phlox to apologize to the Kreetassans and avoided a diplomatic incident. He even told Phlox about his attraction to T'Pol. Phlox endeared himself to Archer when he saved Archer's dog, Porthos. 

Archer returned the favor when an Antaran refused to be treated by Phlox because the Denobulans and the Antarans were mortal enemies. He convinced Phlox to set aside his preconceptions, and attempt to persuade the Antaran to accept treatment. Phlox's attempts were successful, and the Antaran gave his consent. 

Phlox and Archer continued their friendship for the rest of Enterprise's mission, depending on each other for not only friendship, but counseling.

Hoshi Sato
A white-knuckled explorer from the beginning, communications officer Hoshi Sato was at first hesitant to reveal her misgivings to her captain. Not long after the discovery of a derelict Axanar vessel in 2151, Archer was able to coax Sato into describing her fears. While Archer was sympathetic, he nevertheless expected Sato to perform her duties and placed confidence in her abilities in diffusing a situation involving an attacking Axanar vessel. Taking strides to overcome her difficulties, Sato would later make it a point to volunteer for missions, offering to join T'Pol and Malcolm Reed on a severely damaged Klingon starship, and later opting to stay alone with the alien Tarquin for a short time in 2153. 

Hoshi was Archer's choice for looking after Porthos before surrendering himself to the Suliban Cabal in 2152. 

By the end of the Xindi mission, Sato had become one of Archer's most valued officers, ultimately aiding him in disarming the Xindi superweapon despite having been injured by Xindi-Reptilians. 

Maxwell Forrest
Admiral Maxwell Forrest was Archer's mentor and fully trusted him as a capable starship captain devoted to the mission. When the Vulcans, and in particular Ambassador Soval, objected to Archer returning Klaang back to Qo'noS, Forrest backed Archer up and gave him the Enterprise assignment, asking him to "[not] screw this up". After the success of the mission, he was so pleased that Enterprise got the green light to continue its mission of exploration and First Contact. 

In 2154, when the Enterprise returned home from the Delphic Expanse, he forced Archer to apologize to Soval after an emotional outburst in debriefing, maintaining the respect Forrest had for Archer. 

He and Admiral Forrest remained close friends until the Admiral's death on Vulcan when the United Earth Embassy was bombed by what was assumed to be Syrrannite terrorists. 

Travis Mayweather
In many ways, Archer was a role model for his young helmsman, Travis Mayweather. Following the death of Mayweather's father in 2152, Archer personally comforted Mayweather, and granted him permission to visit his family aboard the. 

During their time in the Delphic Expanse, Mayweather was one of the few officers to whom Archer opened up. As the Enterprise neared Azati Prime, Archer refused to allow Mayweather to go on what amounted to a suicide mission, choosing to go himself. He confided in Mayweather that he had asked for too many sacrifices already, opting to pay what Mayweather described as a penance. 

Romance
In 2136, when Archer was 24 years old and in flight school in San Francisco, he met Margaret Mullin, with whom he became romantically involved. The night before he graduated, he asked her to marry him. Margaret turned him down as she did not want to become "a Starfleet widow." 

Some time prior to 2143, Archer had a relationship with Caroline. When she moved to New Berlin, however, he decided to get drunk in the 602 Club. 

Later in the 2140s, Archer was romantically involved with Erika Hernandez. However, he discontinued the relationship when he became Erika's superior officer. In 2154, after Erika became captain of the, they briefly rekindled their romance. 

In 2151 Archer had a brief romantic relationship with Riann: an Akaali female he met when they made First Contact with their civilization. When his translator malfunctioned and he was in danger of being exposed as an alien, Archer quickly kissed her to prevent her from asking questions. When later on they got to know each other better and came closer and he was about to leave the planet, he kissed her again while she joked that the translator must have malfunctioned again. 

Porthos
Porthos was Archer's pet beagle–his "buddy" as he once called it–and he had him since he was six weeks old. Archer's girlfriend's mother had a beagle that he was particularly crazy about. Even after her daughter and he broke up, he stayed in touch with the mother. When the dog got pregnant, he was the first one she called. Four males in the litter, the four Musketeers as they were called. . Porthos lived with Archer on Earth in mid-2150 before moving to Enterprise in April of 2151. 

On Enterprise, Porthos has a dog basket in Archer's quarters as well as a mat he could lie down on in the captain's ready room. Archer also kept a small supply of cheese in a cupboard, something he gave Porthos as a treat now and then, until he realized the "treat" was causing him mild gastrointestinal distress. 

Aware that Porthos needed to get off the ship from time to time, Archer occasionally allowed him to visit habitable planets and took him on certain away missions. It was on one such visit to the Kreetassan homeworld that Porthos picked up a deadly pathogen. Archer was incredibly upset that his "best friend" was at risk of death, and stayed at his side until Doctor Phlox could develop a cure. Porthos eventually made a full recovery. 

In 2153, Archer allowed Porthos to accompany Enterprise to the Delphic Expanse in search of the Xindi superweapon to the objection of Commander Tucker who believed the Expanse may have unknown properties which could affect him. Early on during the Xindi mission, it became evident that Porthos could sense the anomalies present in the Expanse. He had attempted to alert Archer to one, however, the captain did not understand the warning until after the anomaly had passed through his desk.

Alternate realities and timelines

 * In 2153 an anomaly infected Archer's hippocampus with interspatial parasites, causing anterograde amnesia by impairing the synaptic pathways that allowed him to form new long-term memories. Though the crew tried to keep Archer up to date so he could function as captain, Starfleet Command eventually relieved him of command; he spent most of his time in his quarters. Earth was destroyed in 2154, but Archer remained on board until 2156, when Enterprise reached Ceti Alpha V. T'Pol took care of him for nine years (she apparently developed feelings for him as time went on, although Archer naturally could not reciprocate them as he would never remember it the next morning), when Phlox arrived from Denobula with a cure. Destroying one of the clusters of parasites, Phlox and T'Pol discovered that destroying them now also destroyed their existence in the past as well, and realized that, by destroying the parasites in the present, they could completely change the outcome of Enterprise's original mission in the Delphic Expanse. As Enterprise was boarded by Xindi forces, Archer initiated a subspace implosion, eradicating the remaining parasites and thus preventing himself from ever having been infected in 2153.
 * In 2154, Enterprise was flung to the year 2037 while en route to the Xindi Council planet. Archer decided that the ship would become a generation ship, and that the crew's descendants would be the ones to complete the ship's mission and stop the Xindi superweapon. Archer eventually married an Ikaaran woman named Esilia. One of his descendants was Karyn Archer.

Awards and honors
In 2154, several dozen North American schools were renamed for Jonathan Archer following the successful resolution of the Xindi crisis, including the former high school of Erika Hernandez. 

Archer earned an impressive list of commendations during his career, including the Starfleet Medal of Valor with clusters, the Star Cross, the Prentares Ribbon of Commendation, and the Federation Citation of Honor. (Biographical display in )

In the 23rd century, historian John Gill hailed Archer as "the greatest explorer of the 22nd century." (Biographical display in )

Two planets were named for the former captain: Archer's Planet in the Gamma Trianguli sector, and Archer IV, the first M-class planet explored by Enterprise. (Biographical display in )

Archer's Comet and the Federation starship USS Archer were also named for the former captain. 

Memorable quotes
"Volatile? You have no idea how much I'm restraining myself from knocking you on your ass."
 * - Archer, to T'Pol the first time he meets her

"We can't be afraid of the wind, Ensign."
 * - Archer to Ensign Mayweather

"Human beings have a code of behavior that applies whether they're Starfleet officers or space boomers, and it isn't driven by revenge. Just because someone isn't born on Earth doesn't make him any less human."
 * - Archer to Mayweather

"Someday... my people are going to come up with some sort of a doctrine, something that tells us what we can and can't do out here, should and shouldn't do. But until somebody tells me that they've drafted that directive... I'm going to have to remind myself every day... that we didn't come out here to play God."
 * - Archer, foreshadowing the Prime Directive

"Once you give up, the game's over."
 * - Archer to Tucker

"An old girlfriend's mother had... this beagle I was crazy about. Even after her daughter and I broke up, we stayed in touch. When the dog got pregnant, I was the first one she called. Four males in the litter - the Four Musketeers. I've had Porthos since he was six weeks old."
 * - Archer, about his "best friend" Porthos

"I don't like bullies, Trip. Not on Earth, and not out here."
 * - Archer to Tucker

"I need what was taken from me. There's too much at stake to let my morality get in the way."
 * - Archer to Orgoth

"I'm prepared to do whatever it takes to find your ship. And if that ends up causing me remorse, then it's something I'm willing to live with."
 * - Archer to Orgoth

"We'll find a way through this. But I won't leave anyone behind, not if I can help it. I can't try to save humanity without holding on to what makes me human."
 * -Archer to T'Pol

"I need Trip. Trip. I'll take whatever steps necessary to save him."

"Even if it means killing me?"

"Even if it means killing you!"

"You're not a murderer."

"Don't make me one."
 * - Archer and Sim

"You did the right thing."

"It seems the longer we're out here, the more I have to keep telling myself that."
 * -Trip and Archer

"You've changed, Captain."

"And not at all for the better!"
 * - Silik and Archer

"Up until about a hundred years ago... there was one question that burned in every Human - that made us study the stars and dream of traveling to them: "Are we alone?" Our generation is privileged to know the answer to that question. We are all explorers, driven to know what's over the horizon, what's beyond our own shores. And yet... the more I've experienced, the more I've learned... that no matter how far we travel, or how fast we get there... the most profound discoveries are not necessarily beyond that next star. They're within us - woven into the threads that bind us - all of us - to each other. The final frontier begins in this hall. Let's explore it together."
 * - Archer, speaking to alien delegates

"Here's to the next generation."
 * - Archer, proposing a toast to the future

Key dates

 * 2112: Born in upstate New York on Earth to Henry and Sally Archer
 * 2124: Henry Archer dies of Clarke's Disease
 * 2143: Along with A.G. Robinson, becomes the first Human to achieve warp 2.5
 * 2150: Becomes commanding officer of the starship
 * 2151: Enterprise launches
 * Becomes one of the first Humans to set foot on Qo'noS
 * Makes first contact with the Suliban
 * Makes first contact with the Andorians
 * 2152: Begins second year of deep space exploration, commanding Enterprise
 * Travels to the 31st century and learns he will become an important part of the formation of the United Federation of Planets
 * Makes first contact with the Tholians
 * Put on trial on Narendra III by the Klingons
 * Makes first contact with the Tellarites
 * 2153: Given the mission to destroy the Xindi superweapon
 * Transformed into a Loque'eque
 * Travels back in time to the year 2004
 * 2154: Completes the mission in the Delphic Expanse by destroying the Xindi superweapon
 * Travels to the mid-20th century
 * Holds the katra of Surak for a short time
 * Makes first contact with the Organians
 * Transformed into a Klingon hybrid
 * 2155: Attends the opening ceremony of the Coalition of Planets
 * 2161: Final year commanding Enterprise
 * Helps rescue the daughter of Shran
 * Signs the Federation Charter
 * 2169: Becomes Federation Ambassador to Andoria
 * 2175: Serves as Federation Councillor
 * 2184: Is elected Federation President
 * 2192: Steps down as Federation President

Appearances
Jonathan Archer appears in:
 * Star Trek: Enterprise (Every episode, First appearance)

Background information
Archer's first name was originally to have been "Jackson". This was eventually switched to "Jonathan", as research turned up exactly one person in the United States of America with the name of "Jackson Archer." (Cinefantastique, Vol. 33, No. 5, p. 21)

While the character of Archer was planned to have the first name "Jackson", a character breakdown sheet sent from Paramount Pictures to talent agents, upon seeking an actor to play the role, described the character thus; "Early 40s. Physical. Bold personality. Intensely curious. Born and raised an explorer. Unlike the Starfleet captains in centuries to come, he exhibits a sense of wonder and excitement, as well as a little trepidation about the strange things he will encounter. He holds a grudge against the Vulcans, who he blames for impeding humanity's progress. But his science officer is Vulcan, and he's struggling to reconsider those preconceptions. Although he has a strong sense of duty, he's a bit of a renegade – he's not afraid to question orders or even disobey them if he feels in his gut that he's right...."

The script for establishes that Archer is nine years old in the very first scene of Enterprise and thirty-nine in 2151. When the adult version of the character is introduced in the script, the teleplay quotes a section from the character breakdown, stating, "Unlike the Starfleet Captains in centuries to come, he exhibits a sense of wonder and excitement."

Jonathan Archer was played by Scott Bakula in all 98 episodes of Star Trek: Enterprise. The young Jonathan Archer in the pilot episode was portrayed by Marty Davis.

Archer's hairstyle changed, during the course of the series, from a classic comb-over to a shorter, straight-banged haircut that he ended up sporting by the conclusion of the show's third season. Between production of that season and the fourth one, hair designer Michael Moore commented, "The short hair on him was a good move. When we first started, they went with the traditional cut kind of longer, part to the side and all. It kind of morphed into what it is now. We just blow it dry really quickly with a little product in there to give it a little texture so it doesn't lay down flat or anything. That's the extent of his look–pretty no-nonsense." (Star Trek: Communicator issue 152, p. 30)

In November 2012, Brannon Braga stated on his Twitter account that the show's fifth season would have revealed the mysterious Humanoid Figure (aka Future Guy) in the Temporal Cold War to be Jonathan Archer "trying to correct history." 

Apocrypha
The novel Beneath the Raptor's Wing gives Archer's middle name as "Beckett".

In the Star Trek: Myriad Universes novel, A Less Perfect Union, John Frederick Paxton destroys Starfleet Command and ends the talks for the Coalition of Planets. Archer continues to work toward creating a political alliance between Vulcan, Andoria, Tellar and other worlds, with the belief Earth would eventually join as well. His actions are opposed by the Isolationist Party, who has taken control of the Parliament and recalls him for court martial. In this novel, he also performs the marriage between Trip Tucker and T'Pol. He also marries Erika Hernandez sometime prior to 2199 and died sometime after 2244.