Three years into their five-year mission, the crew of the arrives at the massive Federation starbase Yorktown for a period of rest. Captain James T. Kirk, feeling weary of the repetitive nature of deep-space exploration, has applied for a promotion to Vice Admiral, while Commander Spock is grappling with the news of Ambassador Spock's death and his own future on New Vulcan.
The crew discovers that Krall is searching for the , an ancient bio-weapon that Kirk recently acquired. They eventually learn that Krall is actually Balthazar Edison , the former captain of the Franklin. Feeling betrayed by the Federation's shift from war to diplomacy, he has used alien technology to prolong his life and now intends to destroy Yorktown and the Federation.
In a climactic battle, the crew uses the repaired USS Franklin and a blast of "classical" music (Beastie Boys' "Sabotage") to disrupt Krall’s swarm. Kirk eventually stops Krall from releasing the bio-weapon inside Yorktown's life-support system. In the aftermath, Kirk and Spock both decide to remain with Starfleet as they begin construction on a new ship: the .
