Plot

The crew of the USS Enterprise explores the furthest reaches of uncharted space, where they encounter a new ruthless enemy, who puts them, and everything the Federation stands for, to the test.

After stopping off at Starbase Yorktown, a remote outpost on the fringes of Federation space, the USS Enterprise, halfway into their five-year mission, is destroyed by an unstoppable wave of unknown aliens. With the crew stranded on an unknown planet and with no apparent means of rescue, they find themselves fighting against a ruthless enemy with a well-earned hatred of the Federation and everything it stands for. Only a rebellious alien warrior can help them reunite and leave the planet to stop this deadly menace from beginning a possible galactic war.—Paramount Pictures

Getting through the first half of their five-year mission, Captain Kirk and the USS Enterprise crew now venture into uncharted territories. They arrive at Starbase Yorktown for shore leave, Kirk intends to be promoted to Vice Admiral to remain there and has recommended Spock for his present position as ship's captain. After a devastating attack by a massive army of unknown aliens, Kirk and his crew find themselves stranded on an unknown planet with no means of contacting the Federation or each other. The alien warlord Krall seeks an ancient weapon called the Abronath that Kirk has kept after an unsuccessful diplomatic mission. Reunited and aided by the alien warrior Jaylah, Kirk and crew must fight to survive and take on this deadly menace with a strong hatred for the Federation. Will they be able to destroy the new danger before it's too late?—Blazer346

Captain James T. Kirk (Chris Pine) acts as a diplomatic intermediary on a mission to negotiate a treaty between the Teenaxi and the Fibonans who are longtime enemies. He offers the Teenaxi a piece of an ancient weapon as a gesture of goodwill and a proposal for truce. The Teenaxi attack Kirk when they do not trust the Fibonians (and believe the weapon to be stolen), but he beams off the planet. While walking down the corridor, Kirk asks his first officer to store the weapon into the ship's archive vault.

Three years (966th day) into its five-year mission, the USS Enterprise arrives at Starbase Yorktown, a massive (newest and the most advanced) space station, for resupply and shore leave for her crew. Kirk is exhausted with the endless routine of space travel and can no longer distinguish when one day ends and the next one begins. They continue to search for new life forms in order to establish firm diplomatic ties. Prolonged cohabitation has complicated inter personnel dynamics. Some experiences for the better, and some experiences for the worse. Kirk knows that he joined Starfleet on a dare, unlike his own father, who believed in its mission and its principles.

Struggling to find continued meaning in the endless nature of their mission of exploration (he believes that the universe is truly endless and so exploration has a great deal), Kirk has applied for a promotion to Vice Admiral and commanding officer of Yorktown. He recommends Spock (Zachary Quinto) as the new captain of the Enterprise. Meanwhile, Hikaru Sulu (John Cho) reunites with his family, Montgomery Scott (Simon Pegg) works to keep the ship operational, and Spock and Nyota Uhura (Zoe Saldana) amicably end their relationship; Spock also receives word from New Vulcan that Ambassador Spock (Spock's future self from the original timeline) has died.

The Enterprise is dispatched on a rescue mission after an escape pod drifts out of a nearby uncharted nebula. The survivor, Kalara (Lydia Wilson), claims her ship is stranded on Altamid, a planet within the nebula. She says that the ship was on a scientific mission inside the nebula when is malfunctioned and crash landed on the planet. Once inside the unexplored nebula, the Enterprise has communications with Starfleet blocked. The Enterprise reaches Altamid, which shows massive underground activity, but no life forms on the surface. The rescue turns into an ambush when the Enterprise is quickly torn apart by a massive swarm of small ships.

The ships have a tough outer shell which penetrates the Enterprise's hull without any resistance. The phasers have no effect, and the torpedoes cannot track their movements. The ships attack and detach the warp nacelles. The swarm's leader, Krall (Idris Alba) (Captain Balthazar Edison), and his crew board the crippled Enterprise. Krall takes control a relic called the Abronath that Kirk had obtained for the diplomatic mission to Teenaxi. Kirk manages to attack Krall and wrest back control of the Abronath, as Krall is weakened with prolonged exposure to the Earth-like atmosphere. Scotty manages to reroute the reserve power to the impulse engines to provide some control on the Enterprise. As the Enterprise tries to escape into the nebula, Krall orders an attack to cut the saucer section connection to the warp core and cut off its source of power.

Scotty is launched into space in an escape pod, but Krall captures and removes many crew members from the ship (they capture the escape pods from the ship as well). Kirk then orders for the crew to abandon ship as the Enterprise's saucer section hurtles towards the planet. Kirk gives the Abronath to a crew member to hide. Uhura pushes Krall (who got the empty shell of the Abronath and realize that Kirk hide the weapon) into an escape pod with herself and ejects before he can get to Kirk. As the ship is doomed, Kirk orders full evacuation. Kirk is the last one to leave just before the saucer crashes into the planet. During their escape, different crew members land on different parts of the planet.

On the planet's surface, Sulu, Uhura, and other survivors are captured by Krall. Sulu and Uhura manage to escape from their prison and find that Krall possesses a great deal of Federation technology. Sulu finds that Krall had hacked into the Yorktown database and had been tracking the Enterprise from the beginning. They manage to send a distress signal to Yorktown but are then captured. Krall says that the distress signal had incorrect coordinates, which means the Yorktown fleet will be stranded in the nebula and the base will be defenseless. Krall says that his attack on the Federation will spread from Yorktown.

Kirk and navigator Pavel Chekov (Anton Yelchin), accompanied by Kalara, locate the wrecked saucer section. Kalara claims to be the captain of the ship that was attacked by Krall and claims that he is holding her crew hostage until she delivered the Enterprise to him. Kalara leads Kirk and Chekov back to the Enterprise. Kirk wanted to use the ship's scanners to search for the crew. Kalara is revealed to be Krall's spy when she tries to retrieve the Abronath as she did not know that Kirk had already hide it. To escape Krall's soldiers, Kirk activates the still-functional thrusters, causing the saucer to lurch forward, crushing Kalara. Kirk tracked the call Kalara made to Krall and found the location of his base.

Meanwhile, a wounded Spock and Dr. Leonard McCoy (Karl Urban) search for other survivors. Spock confides to McCoy that he intends to leave Starfleet to continue the late Ambassador Spock's work on New Vulcan. This is also the reason he broke up with Uhura. Spock and McCoy find a cave which has carvings similar to the Abronath, indicating that it came from the planet. Meanwhile, Scotty is attacked by hostiles on the planet, who also crash landed there just like the Enterprise. He is rescued by Jaylah (Sofia Boutella), a scavenger who previously escaped Krall's base where her father was killed. Jaylah says that Krall is searching the stars for a death machine. She takes Scotty to her makeshift home, the grounded USS Franklin, an early Starfleet vessel reported missing over a century earlier. She was the first Federation vessel capable of Warp 4 and went missing in the Gagarin Radiation Belt in the 2160s.

Kirk and Chekov activate one of Jaylah's traps and are reunited with Scotty, and then use the Franklin and find a transmission from McCoy. Spock and McCoy are also found. They determine the crew's location using the unique vokaya mineral on the necklace that Spock had gifted Uhura. Using the ship as a base, they come up with a plan to raid Krall's base and transport the crew to the Franklin, then escape the planet in the repaired ship. Meanwhile, while reading Kirk's logs, Krall realizes that Kirk hide the Abronath with the crew. He threatens to execute them and forces Ensign Syl (Melissa Roxburgh) to hand over the Abronath that she had kept hidden for Kirk (she hide it in her brain as she opens up her cranial appendages). The Abronath is the missing half of an ancient bioweapon, created by the planet's original inhabitants which can disintegrate any humanoid. Krall demonstrates the Abronath to Uhura using Syl as a specimen. With the device complete, Krall intends to attack Yorktown and kill its inhabitants, and, using Yorktown's advanced technology, go onto attack the Federation.

Kirk and the others free the crew as Krall launches into space with the bioweapon, leading his swarm fleet to Yorktown. Krall's soldiers attempt to stall Kirk and his crew as much as possible but are outnumbered. As everyone is transported out, Kirk remains as Jaylah has been engaged by one of Krall's soldiers. Kirk rescues Jaylah and she understands the meaning of being part of a crew. The Enterprise crew pursues Krall on the Franklin into space (after Sulu drops the ship from a cliff, by using the impulse engines, in order to jump start the warp engines). Spock determines that the swarm is coordinated and hence must rely on some frequency of communication. If the communication is disrupted, the swarm maybe defeated.

Scotty transports Spock and McCoy into one of Krall's swarm ships. After dispatching the drones, they learn that VHF transmissions can disrupt Krall's communications and destroy his fleet. Matching the drone fleet's frequency (57.7 megahertz) and using the 'classical' song "Sabotage" by the Beastie Boys, they destroy almost the entire fleet. Krall and his three surviving ships crash into Yorktown. As Krall flees into the city, Uhura and Kirk discover from the Franklin's logs that Krall is actually Balthazar Edison, the former captain of the Franklin. A pre-Federation human soldier, Edison was bred on war. He became disillusioned with the newly founded Federation, rejecting its principles of unity and cooperation with former enemies.

When he and his crew were stranded on Altamid by a rogue wormhole, Edison believed the Federation had deliberately abandoned them. The three survivors prolonged their lives with the technology of the planet's extinct natives (at the cost of their human physiology and their numerous victims' lives), and re-purposed that species' dormant drone workers into the swarm. Edison now plans to destroy the Federation to resume galactic conflict. Kirk pursues Edison into Yorktown's ventilation system, where Edison activates the bioweapon. Before it can be unleashed, Kirk ejects the weapon and Edison into space, where the weapon disintegrates Edison. Using their commandeered swarm ship, Spock and McCoy save Kirk moments before he is also blown into open space.

In the aftermath, Commodore Paris (Shohreh Aghdashloo) closes the files of Captain Edison and the crew of the USS Franklin. Kirk opts to remain as captain, and Spock chooses to remain in Starfleet and resumes his relationship with Uhura. Jaylah is accepted into Starfleet Academy based on Kirk's recommendation. As the crew celebrates Kirk's birthday, they view the construction of their new ship, USS Enterprise-A, and after its completion, they depart to resume their five-year mission.