Stardate 2263: Captain Kirk offers an ancient artifact that is said to be a weapon as a peace gift to an alien civilization, but they refuse and attack him. Upon his premature return, the device is stored in an archive drawer on the Enterprise. The time is three years into the Enterprise's five-year mission. As his 30th birthday approaches, Kirk is tired of space travel and plans to apply for the position of vice admiral of Yorktown, a huge starbase on the edge of the Federation. The Enterprise is docked at Yorktown when a lifeboat with an alien woman is rescued from space. The woman, Kalara, says her ship was lost on the other side of a nebula, so the Enterprise is sent to rescue the other crew members. As the Enterprise arrives at the destination, a planet called Altamid, the ship is attacked by a huge swarm of small vessels that cut their way through the hull. The attackers sever the nacelles. The alien leader, Krall, appears aboard, beginning to search for the ancient artifact. But Kirk can hide the device from him. Scotty manages to divert warp power to the impulse engines to escape, but then the attackers cut off the Enterprise's neck. In order to stabilize the ship, Kirk, with the help of Uhura, separates the saucer from the remains of the neck. But Uhura is captured by the attackers. The surviving crew members abandon the ship, but the Swarm ships snatch all escape pods from space, including Sulu's. Scotty escapes in a torpedo, McCoy and Spock hijack one of the Swarm ships, while Kirk, Chekov and Kalara leave the saucer using "Kelvin pods" in the last moment before the crash on Altamid. On the planet, McCoy tends to the wounded Spock. Spock tells the doctor that he learned of Ambassador Spock's death and that he plans to leave the Enterprise to serve New Vulcan. In the meantime, Scotty runs into a young alien woman named Jaylah, who defends him against some attackers with the help of holographic duplicates of herself. She leads Scotty to her "house", a grounded old Federation ship named USS Franklin, and asks him to make it spaceworthy again to escape from the planet. Like many other aliens over the years, she and her family were kidnapped by Krall. Kirk knows that Kalara led the Enterprise into the trap. She promises to cooperate from now. Kirk, Chekov and Kalara board the crashed saucer of the Enterprise in order to scan for the missing crew members. When Kirk pretends to salvage the alien device, Kalara calls Krall's people. Kirk deliberately allowed her to call Krall in order to find out where he is located. Krall's people, however, arrive sooner than expected. In order to escape, Chekov activates the maneuvering thrusters of the Enterprise. He and Kirk escape, whereas Kalara is crushed when the saucer gets overturned. In Krall's camp, Uhura has to witness how Krall "sucks the life" out of his prisoners to regenerate. She and Sulu briefly manage to break free. They discover that Krall is monitoring Federation channels and obviously plans to attack Yorktown. But before they can act, Krall apprehends them again. He threatens to kill Sulu if no one points him to the whereabouts of that old device, the Abronath. An alien Enterprise crew member, Syl, opens the tentacles on her head where Kirk put the device. Krall takes the Abronath and completes a lethal biological weapon, which he tests on Syl. Some of the crew reunite on the Franklin as Kirk and Chekov run into one of Jaylah's traps and Scotty puts the old transporter into operation again to beam out McCoy and Spock. Spock locates Krall's camp scanning for a Vulcan mineral in Uhura's talisman. The transporter of the Franklin, however, is not capable of beaming out the missing Enterprise crew members because of lacking signal strength. So Kirk takes a motorbike to create a diversion with holographic copies of himself, while Jaylah, Scotty and Spock release the prisoners. Jaylah loses her transporter beacon fighting against Manas, one of Krall's aides who once killed her father. Kirk remembers that he promised to leave no one behind and grabs her hand mid-air during a jump with his motorbike so both can be beamed out. Krall and the Swarm, however, have already left the planet to attack Yorktown and kill all of its inhabitants. Scotty reactivates the engines of the Franklin so the crew of the Enterprise can follow the Swarm. But it would be a totally hopeless battle. Spock and McCoy, the two crew members who are a bit familiar with the technology, beam over to a Swarm ship again to examine the possibilities. They find out that a strong high-frequency signal transmitted to the Swarm could disrupt it. Scotty has the idea for a radio transmission of "Sabotage" by the Beastie Boys. Once the music plays, the Swarm ships all collide and explode - except for three, one of them manned by Krall. Krall enters the atmosphere of Yorktown to release the bioweapon, but Kirk takes the Franklin into the flight path so the small vessels get stuck in the old ship's hull. Krall survives the crash. In an old recording from the Franklin Uhura identifies Krall: It is the captain of the Franklin, Balthazar Edison. He was one the three last survivors of the ship and managed to live on on Altamid with the help of life-prolonging technology that some aliens left behind. He holds a grudge against the peaceful nature of the Federation and wants to incite a war. Kirk can keep him from releasing the bioweapon in Yorktown's ventilation system. Krall is blown out into space where the bioweapon dissolves his body, whereas McCoy and Spock rescue Kirk with a Swarm vessel. Sulu is reunited with his husband. The two, like Jaylah and the remainder of the crew, join Kirk's birthday party. Kirk declines the offer to become the vice admiral of Yorktown. He and his crew are looking forward to their voyages on the new starship, the USS Enterprise NCC-1701-A.