Stardate 2259.55: The Enterprise is hiding in an ocean on the planet Nibiru, while Spock is on a mission to stop the activity of a volcano using a cold fusion device, in order to save the local population. When it turns out impossible to retrieve Spock otherwise, Kirk orders the Enterprise to surface and beam out Spock, which is witnessed by the primitive inhabitants and hence violates the Prime Directive. Spock, however, reports the incident, which leads to Kirk's demotion to Christopher Pike's first officer. In the meantime, a mysterious man named Harrison has bribed a Starfleet officer to blow up a Starfleet archive in London, the price being the cure of the man's ill daughter. The leading officers of Starfleet come together in a meeting in San Francisco, which is attacked by Harrison and costs Pike's life. Kirk can bring down the attacking vessel, but Harrison escapes to Qo'noS. In order to eliminate the terrorist, Admiral Marcus orders Kirk to take the Enterprise to the Klingon border and fire torpedoes at Harrison's hiding place in an abandoned city. The crew, however, is opposed to the torpedoes. Scotty is even relieved of duty because he sees the torpedoes, which are impervious to scans, as a danger he can't control. Kirk eventually gives in to the objections and embarks a captured civilian vessel to apprehend Harrison, together with Spock and Uhura. Uhura tries in vain to convince the Klingon patrol to provide support against Harrison, upon which Harrison kills all the Klingons and surrenders to the Starfleet crew. The Enterprise is dead in space due to a malfunction of the warp core, which is suspected to be sabotage. Harrison turns out be be Khan Noonien Singh, a genetically enhanced human being from the 20th century, and the 72 torpedoes actually hold the cryonic chambers with his followers. Admiral Marcus appears with a huge vessel, the Vengeance. He threatens to destroy the Enterprise, along with Khan who helped him build the ship and the torpedoes in the first place, working for the secret organization Section 31. Carol Marcus, who has faked her transfer orders to the Enterprise in order to keep an eye on the torpedoes, tries in vain to convince him to cease the attack. Her father beams her over to his ship. Only Scotty's sabotage to the Vengeance prevents the Enterprise's destruction. Kirk joins forces with Khan, and they dive over to the Vengeance where Scotty opens a hatch for them. Kirk tells Scotty to stun Khan once they reach the bridge, but Khan breaks free and kills Admiral Marcus. Kirk negotiates a deal with Khan: the lives of the Enterprise crew for the lives of his 72 people in the torpedoes. Khan fires at the Enterprise regardless once the torpedoes are aboard the Vengeance, but he isn't aware that they have been activated, largely destroying his ship as well. The cryonic chambers, on the other hand, were removed in the meantime and are safely stored aboard the Enterprise. The Enterprise, however, is without power now and falls toward Earth. Kirk reactivates the warp core but is exposed to a fatal radiation dose. Khan makes his ship crash into San Francisco, and he escapes yet again, followed by Spock who is determined to kill him. Dr. McCoy, however, finds out that Khan's blood cells could cure Kirk. He puts Kirk into one of the cryonic chambers to keep his brain intact. So Khan is apprehended alive, and Kirk can be saved. One year later, the Enterprise is relaunched and departs to a mission in deep space, while Khan is back in his cryonic chamber again, joining his people.