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The militarization conspiracy was a plot by Section 31 to militarize Starfleet in the wake of the destruction of Vulcan to prepare for war against the Klingon Empire. Admiral sought this by utilizing the intellect of the revived war criminal. When this backfired with tragic results, Marcus went to extreme lengths to cover up the conspiracy all while exploiting opportunities to begin his war.

Conspiracy
Following 's destruction in 2258, Section 31 went in search for potential weapons to better defend the Federation and located the SS Botany Bay, recovering its seventy-three surviving occupants. Marcus awoke Khan from cryogenic stasis, and (giving him the alias "John Harrison") blackmailed him into designing ships and weapons to prepare for the coming war. Among them was the USS Vengeance, an experimental warship. Disgruntled, Khan attempted to smuggle his crew in the advanced long-range torpedoes he designed, but when he was discovered, he was forced to flee alone. Assuming that, without his cooperation, Marcus would make good on his threat to his crew, Khan plotted revenge.

Revenge
"Harrison" coerced Thomas Harewood into bombing Section 31's base in London. Harewood's daughter Rima was terminally ill, and Harrison promised a blood transfusion in return for Harewood's cooperation. After Harrison kept his promise, restoring Rima to full health, Harewood fulfilled his end of the bargain by going to work and detonating a bomb disguised as a Starfleet Academy ring. Before killing himself, Harewood messaged Marcus to inform him of who had threatened him. 42 lives were lost in the bombing: during the chaos, Harrison salvaged a portable transwarp beaming device from the rubble.

At an emergency meeting at the Daystrom Conference Room in Starfleet Headquarters, Marcus declared a manhunt for Harrison. In attendence were Admiral, captain of the USS Enterprise, and his first officer , who questioned why Harrison would attack a public archive. He then realized Harrison was aware protocol dictated a summit like this one, just as the perpetrator arrived in the jumpship 208.Harrison laid waste the conference, killing Pike and several others before escaping to the uninhabited Ketha Province of Qo'noS, using the confiscated transwarp beaming formula.

Cover-up
When found the transporter in the wreckage of Harrison's ship and learned where Harrison had gone, Marcus gave a vengeful Kirk permission to hunt down and kill Harrison, all while sensing an opportunity to exploit the tragedy. The Enterprise was loaded with Khan's 72 experimental photon torpedoes, still containing the other Botany Bay crewmembers. These would be fired from the edge of the Klingon Neutral Zone to execute him, removing all evidence of the scheme. The crew would not be allowed to examine the torpedoes, while Marcus had Enterprise's warp core sabotaged, intending for the Klingons to find the ship and hold them responsible for the missile barrage. With the two powers now at war, Marcus would have just cause to continue his militarization of Starfleet and conquer the Klingon Empire.

Kirk's crew expressed dubiousness at executing Harrison without trial: called it immoral, while Scott, fearful of what the organization he enlisted in had become, requested a leave of absence. Dejected, Kirk chose land on Qo'noS and apprehend Khan, rather than execute him without a trial. Unfortunately, the Enterprise's warp drive unexpectedly failed, stranding the Starfleet vessel in the heart of the Klingon Empire. Kirk opted to proceed with the mission anyway, despite Chief Medical Officer 's urging that he not "rob a bank when the getaway car has a flat tire."

When Kirk's away team found him, Harrison killed the members of a Klingon patrol that had intercepted Kirk's away team, and then submitted to Kirk's authority. Aboard the Enterprise, Khan explained his involvement with Marcus, after McCoy and discovered his crew of Augments were contained inside the missiles supplied by the admiral. Additionally, Kirk was given coordinates which he passed to Scott, who still possessed enough goodwill towards his former captain to investigate them. He discovered the Io Facility where the Vengeance was being constructed.

Battle over Luna

 * Main: Battle of Luna

Marcus soon arrived on the Vengeance to greet the Enterprise in Klingon space, and ordered Kirk to hand over Harrison to prevent the conspiracy from being exposed. Kirk revealed he knew who Harrison was, and ordered the Enterprise to escape at warp, heading to Earth to expose Marcus.

The faster Vengeance caught up to the Enterprise at warp and crippled the ship while in orbit of Luna. Fortunately, Scott had stowed away on the Vengeance and managed to deactivate its weaponry in time to prevent Marcus from destroying the Enterprise, giving Kirk and Khan time to space-dive and commandeer the ship. Khan then betrayed Kirk, killing Admiral Marcus and threatening to resume bombarding the Enterprise, unless his still-frozen crew was beamed aboard. McCoy removed the cryo-chambers from the missiles, unbeknown to Khan at that point, before they were beamed aboard the Vengeance, saving Khan's crew. The away team returned to the Enterprise, but Khan reneged on the deal, forcing Spock to remotely detonate the missiles and cripple the Vengeance.

The two starships, both critically damaged by the brutal fighting, were caught in Earth's gravitational pull and began hurtling toward the surface. Kirk reactivated the Enterprise's warp core before it crashed, but at the cost of fatally poisoning him. Meanwhile, Khan – believing his crew to be dead – directed the Vengeance to crash into San Francisco, in one final act of spite against his former masters. The enormous ship cut through the city, obliterating landmarks like Alcatraz Penitentiary and killing many civilians. Spock beamed down to execute Khan in retribution for Kirk's death, but McCoy realized Khan's blood could be used to revive Kirk, so beamed over to stun Khan repeatedly in order for Spock to simply knock him out.

Aftermath
McCoy performed a blood transfusion, reviving Kirk. Khan was placed back in stasis with the rest of his crew.

Nearly a year later, Kirk held a memorial for the lives lost as a result of Khan and Admiral Marcus' actions. At the event, Kirk made a speech in which he spoke out against what Section 31 represented and reminded the attendees of the memorial that Starfleet's true mission was the exploration of the galaxy. Shortly afterward, he returned to the Enterprise, to begin the first five-year mission. 

Background
Co-writer Damon Lindelof said the militarization plot in Star Trek Into Darkness came about because they need to acknowledge the events of, but "obviously we don't want Starfleet to militarize, so that's going to be the force of antagonism in the movie, is that that's happening, either in secret or openly." The protagonists, the Enterprise crew, would then "have to sort of make an argument against militarization. That being said, that's going to be a hard argument for them to make, because maybe Starfleet should be militarizing. So the bad guy in the movie is going to be a guy who's, like, going one step too far."

Furthermore, it enabled them to bring in Khan in a new way: "The whole reason that we're doing these movies is these things are unfolding somewhat differently. So wouldn't it be cool if Khan actually got woken up before this movie started, and he's in play? Once we came upon that idea, then it became absolutely mandatory to call him something else, because if Kirk and the crew of the Enterprise didn't know who this guy was or were being lied to about his identity, we needed to replicate that process for the audience."

The storyline had real-life parallels to the miltaristic response of President George W. Bush to 9/11. "All that stuff was in the air and I think we weren't trying to make a sociopolitical statement when we wrote the story, but we just started gravitating towards those ideals because that’s what was on the news," said Lindelof. Actor Simon Pegg felt "There is a parallel with the terrorist activities of Osama Bin Laden and the decision to attack Iraq. Iraq had nothing proven to do with 9/11, and yet Bush used that as an excuse to start a war with those people." He also compared Marcus to Bush's vice-president. 

Apocrypha
The Star Trek: Countdown to Darkness comic book series and subsequent issue "Star Trek After Darkness, Part 1" reveal the Mudd Incident was an early attempt to start the war with the Klingons: Robert April would take over the Enterprise, and thereby begin the war by handing the flagship to Kor.