Borg-Species 8472 War

The Borg-Species 8472 War was a brief but highly destructive six-month conflict from mid 2373 to early 2374, fought between the Borg Collective and Species 8472. The war was started by the Borg, who, in their endless voracious hunger for species "worthy of assimilation", invaded Species 8472's realm with intent to assimilate them. But the forces of Species 8472 proved highly superior to those of the Borg, and they destroyed the invaders. They then retaliated with an invasion of the Milky Way Galaxy with intent to destroy all life in it. Their invasion was repulsed only after Captain Kathryn Janeway of the USS Voyager provided the Borg with an effective weapon against them. 

Failed assimilation attempt
In mid-2373, the Borg Collective learned of the existence of a species whose physiology they believed represented the "apex of biological evolution." Designated Species 8472 by the Collective, this newly-discovered race was the sole occupant of an extradimensional realm known as fluidic space. The Borg were determined to assimilate this species, which would bring them closer to their goal of perfection than any other species they assimilated before. The Collective opened portals into fluidic space by creating special quantum singularities using a modulated graviton beam. Borg vessels invaded fluidic space and attacked Species 8472 with the intent to forcibly draw the species into their fold, as they had done with thousands of other species before.

However, when the Borg attempted to assimilate Species 8472, they found that the species was immune to assimilation – their immune system was so efficient that any foreign body cells encountered were immediately destroyed, including Borg nanoprobes. Moreover, since the Borg learned about different species solely by means of assimilation, they were unable to understand or adapt to Species 8472's technology. This organically-based technology was more than a match for Borg defenses. Species 8472's vessels were nearly impervious to all types of conventional weaponry, while their weapons were able to penetrate Borg shields with ease. In short order, they eliminated the invaders. 

Purification
However, the sudden incursion of a hostile alien species in their biologically-homogeneous space was intolerable to Species 8472. They saw their realm as having been contaminated by weak lifeforms, originating from a galaxy full of similarly impure species that were intent on attempting to destroy them. Therefore, Species 8472 determined that the only course of action to protect their genetic integrity and prevent further attacks was to "purge" this galaxy of weakness, that is, destroy all life in it. Hundreds of their vessels began pouring into the Delta Quadrant, from a string of quantum singularities concentrated in a region of Borg space dubbed the Northwest Passage by the crew of the Federation starship USS Voyager. Species 8472's purification campaign began with the extermination of the Borg Collective as the Borg were the first species to contaminate their realm. 

Over the course of five months, Species 8472 attacked and roundly defeated the Borg in a dozen major engagements. The Borg found themselves completely overwhelmed, incapable of inflicting any but the most superficial damage to enemy forces. The Collective suffered catastrophic losses as Species 8472 swept through its territory; they annihilated not only ships but entire assimilated planets. Two examples of their obvious combat superiority came shortly after Voyager's initial foray into Borg space. In one engagement, a single 8472 bioship annihilated an entire fleet of 15 vessels with ease, which was the largest grouping of Borg vessels witnessed by a Federation ship up to that point. In a separate battle that occurred in Borg Matrix 010, Grid 19, the Borg lost eight planets, 312 ships, and 4,000,621 drones. The Collective's complete extermination was projected to be only weeks away. 

An infernal alliance
At that time, the USS Voyager was approaching the limits of Borg space and the Northwest Passage, intending to use the Passage, which had been detected as being devoid of Borg activity, to safely traverse Borg space. While just over a day away from the Passage, they detected the remains of fifteen Borg cubes destroyed by Species 8472, whom they themselves had not yet encountered. Investigating, they discovered a single 8472 vessel amongst the debris. Hopes of finding a new ally against the Borg were quickly dashed after their first contact with the pilot: Voyager barely managed to escape, and their operations officer, Ensign Harry Kim, was almost killed. During the brief exchange, Kes, Voyager 's Ocampa medical assistant, was telepathically contacted by the aliens, resulting in the Voyager crew learning of their plans. Captain Janeway realized that the Borg were no longer the main threat; Species 8472 posed a far greater threat than the Borg had ever done. Ironically, the Borg, the Federation's greatest enemy, were the best chance of stopping the invasion. In a daring move, Janeway decided she would forge an alliance with the Borg; she would offer them a weapon against Species 8472, in exchange for Voyager's safe passage through Borg space.

Janeway's bargaining chip was The Doctor, who had discovered a way to reprogram Borg nanoprobes to avoid detection as foreign bodies by Species 8472's immune system. These reprogrammed nanoprobes would then be able to attack Species 8472 cells, unlike regular nanoprobes. Janeway ordered Voyager into an assimilated star system and began negotiations with the Collective, intending to offer The Doctor's research as tactical data about its enemy, in exchange for safe passage of Voyager through Borg territory. She had all of the data put into The Doctor's holomatrix; she would have him deleted, and the data along with him, if the Borg tried to assimilate Voyager. An agreement was reached; the Borg would escort Voyager through their space, and, while en route, Voyager personnel would assist the Borg in crafting the research into a biological weapon. The first test of the alliance came when a Species 8472 fleet attacked the system during the negotiation. The system was destroyed, but a cube escaped, using its tractor beam on Voyager to tow it out of danger along with it.

In the next several days, Captain Janeway and Lieutenant Tuvok, her chief tactical officer, worked with the Borg drone Seven of Nine, selected by the Collective to act as its representative to make communication between the two groups easier. They developed a method of introducing the nanoprobes via photon torpedoes, essentially converting them into bio-molecular warheads. However, Species 8472 exploited their telepathic connection with Kes to locate the two ships, and learned of the nanoprobes. An 8472 vessel attacked, and the Collective sacrificed the cube to save Voyager, but not before beaming Seven of Nine and a small contingent of drones aboard Voyager to continue the work. Janeway was severely injured in the attack, and Commander Chakotay, her first officer, decided to dissolve the alliance rather than rendezvous with another Borg cube.

The weapon
Running out of time, the Collective decided to force Chakotay's hand by taking Voyager into fluidic space. Seven of Nine commandeered the ship's navigational deflector and used it to open a quantum singularity, through which Voyager was pulled into Species 8472's realm. During this attempt Chakotay ordered Seven of Nine to stop or he would eject the drones into space; however after carrying out his threat, Seven of Nine survived.

Faced with an imminent attack by Species 8472, Janeway, now recovered from her injuries, allowed Seven of Nine to modify Voyager to fire the bio-molecular warheads after relieving Chakotay of duty. The weapon proved effective as all four 8472 vessels attacked were destroyed. The goal completed, Seven of Nine took Voyager back out of fluidic space, after which it destroyed thirteen more 8472 vessels with a high-yield warhead armed with the nanoprobes.

Seven of Nine transferred the specifications of the weapon to the Collective. The demonstration had the desired effect: alarmed at their new-found vulnerability, Species 8472 fell into full retreat on all fronts and began disappearing back into fluidic space. 

Aftermath
Once the invasion had been repelled, the Borg promptly terminated the alliance with Voyager and attempted to assimilate the ship and crew through Seven of Nine. The attempt failed, however, due to advanced planning by Captain Janeway and Chakotay. Chakotay possessed a residual link to a mini-collective of former Borg drones he had encountered months before. He used it to link with Seven of Nine to distract the drone while the chief engineer, Lieutenant B'Elanna Torres sent a power surge through the link, permanently severing Seven of Nine from the hive mind. Cut off from the Collective, Seven of Nine gradually regained her individuality and Humanity. Most of her Borg implants were removed and she became a valued member of the Voyager crew. 

Over the course of the next few months, Voyager encountered at least one member of Species 8472 still in their galaxy. It was being chased by a Hirogen hunting vessel. After holding both the member of the 8472 and the Alpha-Hirogen before Seven beamed the two back onto the hunting vessel. 

Due to the defeat of Species 8472, the Borg were able to continue on their path of assimilation, and some, such as Arturis of Species 116, blamed Voyager's intervention in the war and tried to take revenge for the events. 

On the up side, the defeat of Species 8472 averted an invasion of the Milky Way which could have cost every single life inhabiting the Milky Way Galaxy, although Voyager's crucial role in the conflict caused Species 8472 to begin preparations for an invasion of the Federation. It was not until 2375, when Voyager established diplomatic contact with Species 8472, that these plans were reconsidered. 

The Borg-Species 8472 War stands out as one of the few examples in which the Borg were outmatched in a conventional armed conflict. The long-term ramifications of the contact between the two species remained unclear.