Marcus orders the Enterprise to kill Harrison, arming it with 72 prototype photon torpedoes, shielded and untraceable to sensors. En route to Kronos, the Enterprise suffers an unexpected coolant leak, disabling the ship's warp capabilities. Kirk leads an away team with Spock and Uhura onto the planet, where they are ambushed by Klingon patrols. Harrison dispatches the Klingons, then surrenders after learning the number of torpedoes locked on his location.
On the Enterprise, Dr. Leonard McCoy and Admiral Marcus' daughter Carol Marcus open a torpedo at Harrison's behest, revealing a man in cryogenic stasis. Harrison reveals his true identity as Khan, a genetically engineered superhuman awoken by Admiral Marcus from a 300-year suspended animation to develop advanced weapons for war against the Klingon Empire. Khan reveals Marcus sabotaged the Enterprise's warp drive, intending for the Klingons to destroy the ship after firing on Kronos, giving him a casus belli for war.
The Enterprise is intercepted by a larger Federation warship, the USS Vengeance, commanded by Marcus. Marcus demands that Kirk deliver Khan, but the Enterprise, with a hastily repaired warp drive, flees to Earth to expose Marcus. After the Vengeance intercepts and disables his ship, Kirk offers to exchange Khan and the cryogenic pods for the lives of his crew. Marcus forcibly transports Carol to the Vengeance and orders the Enterprise's destruction. The Vengeance suddenly loses power, having been sabotaged by Montgomery Scott, who infiltrated the ship after following coordinates relayed by Khan through Kirk. With transporters down, Kirk and Khan, with the latter's knowledge of the warship's design, space-jump to the Vengeance. Spock contacts his older self on New Vulcan, who in turn, informs him that Khan cannot be trusted. After capturing the bridge, Khan overpowers Kirk, Scott, and Carol, killing Marcus and seizing control of the Vengeance.
Khan demands Spock to return his crew in exchange for the Enterprise officers. Spock complies but surreptitiously removes Khan's frozen crew and arms the warheads. Khan betrays their agreement critically damaging the Enterprise; however, the Vengeance is disabled following the detonation of the torpedoes. With both starships caught in Earth's gravity, they plummet toward the surface. Kirk enters the radioactive reactor chamber to realign the warp core, saving the ship at the cost of his life.
Khan crashes the Vengeance into San Francisco to destroy Starfleet headquarters. Khan survives the crash and flees but Spock transports down in pursuit. McCoy discovers that Khan's blood has regenerative properties that may save Kirk. With Uhura's help, Spock captures Khan and Kirk is revived.
One year later, Kirk addresses a gathering memorializing the victims of Marcus's machinations where he recites the "where no man has gone before" monologue. Khan is sealed in his cryogenic pod and stored with his crew while Carol joins the crew of a recommissioned Enterprise as it departs on a five-year exploratory mission.