Militarization conspiracy The militarization conspiracy was a plot by Admiral and Section 31 to militarize Starfleet to prepare for war against the Klingon Empire . To realize his goals , Marcus sought to use the savage 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 an opportunity to trigger his war . Origins . Admiral Alexander Marcus , the head of Starfleet in the mid - 23rd century , had long been dissatisfied with the Federation ' s response to the belligerent Klingon Empire . Believing war with the Klingons to be inevitable , he sought to unilaterally transform Starfleet into a military organization . Marcus found the secretive , security - minded Section 31 a willing ally for his conspiracy . Following the loss of in 2258 , Starfleet began scouring deep space for new resources and came across the , containing 73 augmented Humans from the 20th century in cryogenic stasis . Marcus woke their leader , Khan Noonien Singh , and held Khan ' s crew hostage to extort him ( under the alias " John Harrison " ) into designing new ships and weapons . Foremost among these efforts was the powerful warship , built by Section 31 at the Io Facility . Disgruntled , Khan attempted to smuggle his crew to safety by concealing them within advanced long - range torpedo es he had designed . However , he was discovered and forced to flee alone . Khan ' s revenge . Believing that Marcus had made good on his threat to kill Khan ' s crew , Khan plotted revenge on Starfleet . He approached Section 31 officer Thomas Harewood , whose daughter was terminally ill , and offered to save her life if Harewood would destroy a Section 31 facility in London . After Khan fulfilled his part of the bargain , Harewood did likewise by detonating a bomb disguised as his Starfleet Academy ring , killing himself and 41 others . In the ensuing chaos , Khan salvaged a portable transwarp beaming device from the rubble . The bombing mandated a meeting of Starfleet ' s senior leadership at the Daystrom Conference Room in Starfleet Headquarters , where Marcus declared a manhunt for " Harrison " . Having anticipated just such a meeting , Khan commandeered jumpship 208 and attacked , killing and several other officers before he was forced to withdraw by . Khan escaped via transwarp beaming to the uninhabited Ketha Province of Qo ' noS , where Starfleet ostensibly could not follow . Path to war . Devastated by Pike ' s death , Kirk implored Marcus to authorize an off - the - book mission to pursue Harrison . Marcus saw in Kirk the opportunity to eliminate Khan , cover up his conspiracy , and incite war with the Klingons on his terms , all in a single stroke . Marcus instructed Kirk to take the USS " Enterprise " to the Klingon Neutral Zone and kill Harrison using 72 long - range torpedoes , which he knew contained Khan ' s crew . He also arranged for the sabotage of the " Enterprise " s warp core , which would leave her stranded when the Klingons came to investigate the source of the torpedoes ; war would undoubtedly follow . " Enterprise " first officer strongly objected to executing Harrison without trial , and ultimately prevailed on Kirk to arrest Harrison instead . Despite the failure of the " Enterprise " s warp drive , Kirk decided to proceed with the mission . On the surface of Qo ' noS , the " Enterprise " away team ran afoul of a Klingon patrol , who were in turn slaughtered by Harrison . Harrison then surrendered himself , inferring correctly that his crew was still alive from the presence of the torpedoes on the " Enterprise " . Kirk sent a message to Starfleet informing them that he had Harrison in custody , inadvertently alerting Marcus that he was in danger of being exposed . Aboard the " Enterprise " , Harrison revealed his true identity and his involvement with Marcus . At his urging , and opened a torpedo and found one of Khan ' s crew inside . Khan also gave Kirk the coordinates of the Io Facility , which Kirk passed to on Earth . Scott arrived at the drydock as the " Vengeance " was preparing to launch , and sneaked aboard . Battle over Luna . Marcus , commanding the " Vengeance " , confronted the " Enterprise " at the edge of Klingon space and ordered Kirk to hand over Harrison , to which Kirk demurred . After Kirk revealed his knowledge of Khan ' s crew , Marcus concluded that everyone on the " Enterprise " needed to be silenced . The " Enterprise " raced for Earth , bringing evidence of Marcus ' s conspiracy . However , the technologically superior " Vengeance " overtook the " Enterprise " and forced her out of warp near Luna with a phaser barrage , 237 , 000 kilometers short of Earth . Marcus rejected Kirk ' s plea for mercy and prepared to destroy the " Enterprise " , only to find the " Vengeance " s systems disrupted from within by Scott . The temporary lull allowed Kirk and Khan to board the " Vengeance " in environmental suit s . Kirk , Scott , and Khan made their way to the " Vengeance " bridge and seized control , though Marcus remained defiant . Khan promptly turned against Kirk , overwhelmed his team , and murdered Marcus . He then demanded that Spock surrender his crew or face destruction . Spock complied , allowing Khan to transport the 72 torpedoes to the " Vengeance " in exchange for Kirk and the others . Khan opened fire on the " Enterprise " , unaware that Spock had foreseen his treachery and armed the torpedoes , after McCoy removed the cryo - tubes . The explosion of the torpedoes crippled the " Vengeance " . The two starships , both critically damaged , were caught by Earth ' s gravity and began falling toward the surface . Kirk managed to reactivate the " Enterprise " s warp core in time to avert a crash , suffering fatal radiation poisoning in the process . Khan , believing his crew dead , directed the " Vengeance " to crash into Starfleet Headquarters in a final act of spite . The enormous ship plowed through San Francisco , obliterating landmarks like Alcatraz Penitentiary and killing many civilians before coming to a rest . Khan survived the crash and leaped from the wreck in a bid for freedom . Spock pursued him with the intent of killing him to avenge Kirk ' s death . The two fought , though Khan eventually gained the upper hand . Meanwhile , McCoy realized that Khan ' s blood could be used to revive Kirk . beamed down and stun ned Khan repeatedly , allowing Spock to defeat and incapacitate him . Aftermath . McCoy performed a blood transfusion to restore Kirk to life . Khan was placed back into stasis with the rest of his crew . Nearly a year later , Kirk spoke at a memorial for the lives lost as a result of Khan and Admiral Marcus ' actions . In his speech , Kirk reminded the attendees 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 . ( ) The conspiracy ultimately failed since , as Montgomery Scott once stated , Starfleet was not a military organization . ( ) Appendices . Background information . Co - writer Damon Lindelof said the militarization plot in " Star Trek Into Darkness " came about because they needed 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 " " 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 .