The USS Enterprise has been sent to a planet in the Nibiru system to observe a primitive civilization. Captain James T. Kirk violates the Prime Directive when First Officer Spock's life is jeopardized, exposing the Enterprise to the planet's civilization during the rescue. Called back to Earth, Kirk is demoted and ordered back to the academy, however Admiral Christopher Pike, reinstated as commander of Enterprise in Kirk's place, talks his superiors into offering Kirk the position of first officer of the Enterprise. The two attend an emergency meeting at Starfleet Command to discuss the bombing of a secret Section 31 installation in London, perpetrated by former Starfleet agent John Harrison. The meeting is attacked by a gunship piloted by Harrison, killing Pike. Kirk destroys the gunship, but Harrison escapes. Kirk is reinstated as the Enterprise's captain. After discovering that Harrison has fled to the Klingon homeworld of Kronos, Kirk receives orders from Admiral Alexander Marcus to hunt down Harrison. The Enterprise is supplied with 72 prototype photon torpedoes and ordered to fire them at Harrison's location once he is found. However, Montgomery Scott resigns in protest of the new weaponry, and Spock, Dr. Leonard McCoy and Uhura convince Kirk to capture rather than kill Harrison.
Arriving on Kronos, Kirk, Spock and Uhura set out to capture Harrison but are intercepted by Klingons. Harrison kills the Klingons almost single handedly and surrenders after learning that the prototype torpedoes are aimed at him. Returning to the Enterprise, Harrison reveals his true identity as Khan, a genetically engineered superhuman who was awakened from a 300-year-long period of suspended animation[10] by Admiral Marcus to develop advanced weapons for a future war between the Federation and the Klingon Empire. The torpedoes are found to contain cryogenic pods with Khan's crew inside, who had previously been held hostage by Marcus.
The Enterprise is soon intercepted by an unmarked Federation warship, the USS Vengeance, designed by Khan and commanded by Admiral Marcus. Marcus demands that Kirk hand over Khan, but Kirk refuses. The Enterprise starts to warp to Earth to have Khan stand trial, but is attacked by the Vengeance mid-warp, exiting 237,000 kilometres from Earth. With the Enterprise severely damaged, Kirk offers to hand over Khan and the cryogenic pods in exchange for the lives of his crew. Marcus refuses, revealing that it was his intention all along to destroy the Enterprise in his plan to dispose of the superhumans and start a war with the Klingons. The Vengeance prepares to open fire, but suffers a power outage caused by Scotty, who infiltrated the ship after following coordinates given by Khan to Kirk. Kirk having left Spock in command, joins Scotty on the Vengeance after a space-jump with Khan from the Enterprise, and they take control of the bridge. Feeling Khan to be untrustworthy, Kirk and Scotty attempt to incapacitate him but are overpowered. Khan then kills Admiral Marcus and takes control of the Vengeance.
Khan negotiates with Spock, beaming Kirk and his boarding party back to the Enterprise in exchange for the torpedo/cryo-pods, planning to destroy the Enterprise. Spock, incapable of lying, acknowledges to Khan that those were his torpedoes but, did not volunteer that the torpedoes were activated and that he had ordered Dr. McCoy to remove Khan's crew from them, keeping the cryo-pods on the Enterprise. Spock reasoned that this subterfuge was necessary, having learned from Spock Prime (the older version of Spock from an alternate future timeline) that Khan Noonien Singh from his timeline was tyrannical and could not be trusted, and was finally defeated, but only at "great cost." The torpedoes incapacitate the Vengeance, and both damaged starships start descending towards Earth. Kirk re-aligns the Enterprise's warp core, enabling the crew to regain control of the vessel, but suffers fatal radiation poisoning in the process and dies. Khan intentionally crashes the Vengeance in downtown San Francisco, where Spock, is transported down to pursue Khan on foot. McCoy's experiment on a Tribble reveals that Khan's blood contains regenerative properties that may save Kirk. McCoy thus orders Kirk to be immediately cryogenically frozen in order to preserve his brain function. Uhura beams down to prevent Spock from killing Khan.
One year later, a revived Kirk addresses a memorial of the events. Khan has been resealed in his cryogenic pod and stored away with his crew. A rebuilt Enterprise then departs for a five-year mission of exploration.
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