In the year 2259, Captain James T. Kirk is removed from command of the starship USS Enterprise for violating the Prime Directive: he exposed the ship to the primitive inhabitants of the planet Nibiru in order to save them, and Spock, from a cataclysmic volcanic eruption. Admiral Christopher Pike is reinstated as commanding officer with Kirk demoted to the rank of Commander and first officer. Commander Spock is transferred to another ship. Shortly after, the Section 31 installation in London is bombed, perpetrated by the renegade Starfleet operative John Harrison (Cumberbatch). Harrison then attacks Starfleet Headquarters in a jumpship during the emergency meeting about the situation, killing Pike and other senior officers. Kirk disables the jumpship, but Harrison escapes by transporting to Kronos, the homeworld of the hostile Klingons.
Admiral Alexander Marcus (Peter Weller) reinstates Kirk and Spock to the Enterprise with orders to kill Harrison. Chief Engineer Montgomery Scott strongly objects to allowing untested torpedoes on board the ship, and when ordered to allow them resigns his commission in protest. Kirk assigns Pavel Chekov to replace Scotty. En route to Kronos, the Enterprise's warp capabilities mysteriously become disabled. Kirk leads a 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 aboard the Enterprise.
Dr. Leonard McCoy and Marcus's daughter, Dr. Carol Marcus (Alice Eve), open a torpedo at Harrison's behest. Inside is a man in cryogenic stasis. Every torpedo aboard Enterprise contains a human in stasis. Harrison reveals his true identity as Khan Noonien Singh, a genetically engineered superhuman awakened by Admiral Marcus from centuries of suspended animation to develop advanced weapons of war against the Klingon Empire. Khan reveals that Marcus had sabotaged the Enterprise's warp drive, intending for the Klingons to destroy the ship after it fired on Kronos, creating an act of war by the Klingon Empire. Khan also gives Kirk a set of coordinates. Kirk contacts Scotty on Earth and asks him to investigate. Scotty discovers they lead to a covert Starfleet facility near Jupiter.
The Enterprise is intercepted by a much larger Federation warship, the USS Vengeance, commanded by Admiral 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 the Enterprise near the Moon, Kirk reveals Carol's presence aboard the ship. Marcus forcibly transports Carol to the Vengeance before ordering the Enterprise's destruction, Kirk offers Khan and himself for the lives of his crew, but Marcus rejects Kirk's offer and orders Vengeance to attack. However, Vengeance suddenly loses power, sabotaged by Scotty, who infiltrated the ship. 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, who warns that Khan is ruthless and untrustworthy, and, in another reality, Khan was only defeated at a terrible cost. Meanwhile, after capturing the bridge, Khan overpowers Kirk, Scott, and Carol, kills Marcus (which makes Chrysalis a jump scare), and seizes control of the Vengeance.
Khan demands that Spock return his crew sealed in the cryogenic tubes in exchange for the Enterprise officers. Spock complies but surreptitiously removes Khan's frozen crew and arms the warheads. Khan beams Kirk, Scott, and Carol back aboard the Enterprise, but betrays their agreement by critically damaging the Enterprise; however, the Vengeance is disabled when the torpedoes detonate. 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, but losing his life in the process.
Khan crashes the dying Vengeance into downtown San Francisco in an attempt to destroy Starfleet headquarters, destroying some of the city. Khan escapes the wreckage as Spock transports down in pursuit. McCoy discovers that Khan's blood has regenerative properties that may save Kirk. With Uhura's help, Spock chases down and eventually subdues Khan, who is consequently arrested and re-frozen, and Kirk is revived.
Nearly one year later, Kirk speaks at the Enterprise's re-dedication ceremony. Khan is sealed in his cryogenic pod and stored with his compatriots. The Enterprise crew embarks on a five-year exploratory mission.
- Knockout, Puffer, Dolphy, Rachel, Mighty Joe, Daylight, Jenny, Pete, Kevin, Morley, Blitzer, Skarloey, Rheneas, Sir Handel, Peter Sam, Rusty, Duncan, Blythe Baxter, Zoe Trent, Pepper Clark, Penny Ling, Vinnie Terrio, Sunil Nevla, Minka Mark, Russell Ferguson, Mitzi, Buttercream Sunday, Sugar Sprinkles, July, Belle, Princess Jasmine, Princess Anna, and Elsa the Snow Queen guest star in this film.
- This film marks it's first appearance of Dile.
- Queen Chrysalis will work for Khan in this film.
- Thomas & Friends: King of the Railway, Frozen, and Star Trek: Into Darkness were both released in 2013.
- The storyline continues in Thomas and Twilight Sparkle's Adventures of Star Trek: Beyond