The Federation starship USS Enterprise arrives at starbase Yorktown, for resupply and shore leave for its crew. Struggling to find meaning in their exploration, Captain James T. Kirk has applied for a promotion to vice admiral; he recommends Spock as his replacement. Meanwhile, Hikaru Sulu reunites with his family, Montgomery Scott works to keep the ship operational, and Spock and Nyota Uhura have ended their relationship; Spock also receives word from New Vulcan that Ambassador Spock has died.
Enterprise is dispatched on a rescue mission after an escape pod drifts out of a nearby uncharted nebula. Its occupant, Kalara, claims her ship is stranded on Altamid, a planet in the nebula. Upon arrival, a massive swarm of small ships ambushes the Enterprise and quickly tears it apart. The swarm’s leader, Krall, and his crew board the crippled Enterprise, capture and kill many crew members, and attempt to capture the Abronath, a relic recovered during a recent mission. Kirk orders the crew to abandon ship, leaving the disintegrating Enterprise saucer section to crash on Altamid.
On the planet, Krall captures Sulu, Uhura, and other survivors. Kirk and Pavel Chekov, accompanied by Kalara, locate the Enterprise’s saucer section. Knowing that Kalara knew they would be attacked, Kirk tricks her into revealing herself as Krall’s spy. She is killed when Kirk and Chekov escape Krall’s soldiers and flip the Enterprise saucer, crushing her. Elsewhere on the planet, Dr. Leonard McCoy and a wounded Spock search for other survivors. Spock tells McCoy that he ended his relationship with Uhura and is leaving Starfleet to help the Vulcan survivors, and continue the late Ambassador Spock’s work. Jaylah, a scavenger who previously escaped Krall’s encampment where her father was killed, rescues Scott and takes him to her makeshift home, the grounded USS Franklin, an early Starfleet vessel reported missing over a century earlier. Scott is reunited with Kirk, Chekov, McCoy and Spock. Krall coerces the captive Enterprise crew to hand over the Abronath, then uses it to complete an ancient bioweapon. With the device complete, Krall intends to kill Yorktown’s inhabitants, then use the base to attack the United Federation of Planets. Kirk and the others free the crew as Krall launches into space with the bioweapon, leading his drones to Yorktown.
The Enterprise survivors power up the Franklin and launch her in pursuit of Krall. Theorizing the swarm’s system may be vulnerable to high frequencies such as VHF or radio, they jam and destroy the swarm by broadcasting the song “Sabotage” by the Beastie Boys. Krall is chased by the Franklin through Yorktown. Uhura, Kirk and Scotty discover from the Franklin’s logs that Krall is actually Balthazar Edison, Franklin’s former captain. A pre-Federation human soldier, Edison rejected the Federation’s principles of unity and cooperation with former enemies like the Xindi and the Romulans. When he and his crew were stranded on Altamid by a wormhole, the survivors used the extinct natives’ technology to prolong their lives at the cost of the others, and re-purposed the ancient race’s dormant mining drone workers into the swarm. Thinking the Federation had abandoned them, Edison planned to destroy the Federation and resume galactic conflict. Kirk pursues Edison into Yorktown’s ventilation system, where Edison activates the bioweapon. Before it can spread, Kirk ejects it and Edison into space, where the weapon disintegrates Edison. Using a commandeered alien ship, Spock and McCoy save Kirk moments before he is also blown into space.
In the aftermath, Commodore Paris closes the files of Captain Edison and the USS Franklin crew. Though offered the promotion to vice admiral, Kirk decides to remain as a captain; Spock chooses to remain in Starfleet, and renews his relationship with Uhura. On Kirk’s recommendation, Jaylah is accepted into Starfleet Academy. As the crew celebrates Kirk’s birthday, they watch the construction of their new ship, the USS Enterprise-A—and resume their mission.
Star Trek Command 