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|Battle of Luna|
|The USS Vengeance strafing the USS Enterprise|
|USS Enterprise|| Section 31|
| James T. Kirk†|
| Admiral Alexander Marcus†|
Khan Noonien Singh
|USS Enterprise||USS Vengeance|
|Casualties and losses|
| James Kirk (later revived). |
Numerous servicemen on Enterprise.
Severe damage to the Enterprise.
Numerous casualties in San Fransisco.
| Alexander Marcus. |
All hands on Vengeance killed.
Vengeance wrecked in San Fransisco.
Khan Noonian Singh captured.
Following the destruction of Vulcan in 2258, Admiral Alexander Marcus of Section 31 became concerned about Federation security, particularly regarding increasing tensions with the Klingon Empire. Section 31 went in search for potential weapons and located the SS Botany Bay, recovering its seventy-three surviving occupants. Marcus awoke Khan Noonien Singh 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 Dreadnought-class 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.
"Harrison" coerced Thomas Harewood into bombing Section 31's base in London. Khan attacked an emergency meeting in San Francisco, killing Admiral Christopher Pike and several others before escaping to the uninhabited Ketha Province of Qo'noS, using the confiscated transwarp beaming formula. Commander James T. Kirk was given permission by Admiral Marcus to find and terminate Khan. The Enterprise was outfitted with seventy-two stealth photon torpedos, with the intent of using these to execute him from the edge of the Klingon Neutral Zone. However, Kirk opted to land on Qo'noS and apprehend Khan, rather than execute him without a trial as ordered. 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 Leonard McCoy's urging that he not "rob a bank when the getaway car has a flat tire."
When Kirk's away team found him, Khan killed the members of a Klingon patrol that had intercepted Kirk's away team. Khan then submitted to Kirk's authority. Aboard the Enterprise, Khan explained his involvement with Marcus, after McCoy and Carol Marcus discovered his crew of Augments were contained inside the missiles supplied by the admiral. Marcus had been responsible for stranding the Enterprise near Qo'noS, intending for the Klingons to find the ship's crew members 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.
Marcus soon arrived on the Vengeance, and attempted to capture Khan to prevent the conspiracy from being exposed.
Fortunately, Montgomery Scott – Kirk's former chief engineer – 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 Nyota Uhura beamed over to stun Khan repeatedly in order for Spock to simply knock him out.
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. (Star Trek Into Darkness)