In 2250, on the planet Vulcan, a young Spock is accepted to join the Vulcan Science Academy. Realizing that the Academy views his human mother Amanda Grayson as a "disadvantage," he decides to join Starfleet instead. On Earth, Kirk becomes a reckless but intelligent young adult. In 2255, after a bar fight with Starfleet cadets accompanying Nyota Uhura, Kirk meets Captain Christopher Pike who encourages him to enlist in Starfleet Academy where Kirk meets and befriends the cynical doctor Leonard McCoy.
Three years later, Commander Spock accuses Kirk of cheating during his Kobayashi Maru simulation. Kirk argues that cheating was acceptable in this context because the simulation had been designed to be unbeatable. The disciplinary hearing is interrupted by a distress signal from Vulcan. With the primary fleet out of range, the cadets are mobilized. McCoy and Kirk board Pike's ship, the Enterprise. Realizing that the "lightning storm" being observed on Vulcan is similar to the one that occurred at the time of his birth, Kirk breaks protocol to convince Pike that the distress signal is a trap.
Enterprise arrives at Vulcan to find the fleet destroyed and the Narada drilling into Vulcan's core. The Narada attacks the Enterprise and Pike surrenders, delegating command of the ship to Spock and promoting Kirk to first officer. Kirk, Hikaru Sulu, and Chief Engineer Olson perform a space jump onto the drilling platform. Olson is killed but Kirk and Sulu disable it. However, Nero launches "red matter" into the core, creating an artificial black hole that destroys the planet. Spock rescues the Vulcan high council and his father Sarek, though his mother dies.
As the Narada heads toward Earth, Nero tortures Pike to gain access to Earth's defenses, and Kirk is stranded on Delta Vega after attempting mutiny. Kirk encounters an older Spock, who explains that he and Nero are from 129 years into the future when Romulus was threatened by a supernova. Spock's attempt to use "red matter" to create an artificial black hole and consume the supernova was too late, and Nero's family perished along with Romulus. Narada and Spock's vessel were caught in the black hole, sending them back in time. Nero stranded Spock on Delta Vega to watch Vulcan's destruction as revenge for failing to save Romulus.
Reaching a Starfleet outpost, Kirk and Spock Prime meet Montgomery Scott. With the elder Spock's help, Kirk and Scott beam onto the Enterprise. Following the elder Spock's advice, Kirk provokes Spock into attacking him, leading Spock to relinquish command due to being emotionally compromised. After talking with Sarek, Spock decides to help Kirk. While Enterprise hides itself under the gas clouds of Titan, Kirk and Spock beam aboard the Narada; Kirk rescues Pike while Spock uses the elder Spock's ship to destroy the drill. Spock leads the Narada away from Earth and sets his ship to collide with Nero's ship. Enterprise arrives and beams Kirk, Pike, and Spock aboard. The older Spock's ship and the Narada collide, igniting the "red matter" and consuming the Narada in a black hole.
On Earth, Kirk is promoted to the rank of Captain and commanding officer of the Enterprise, while Pike is promoted to Rear Admiral. Spock encounters his older self. Having selected a planet for the surviving Vulcans to colonize, the older Spock persuades his younger self to continue serving in Starfleet, encouraging him to do what feels right instead of logical. Spock remains in Starfleet and becomes first officer under Kirk's command. Enterprise goes to warp as the elder Spock narrates the "where no-one has gone before" monologue.