Part 1
In 2267, the USS Enterprise arrives at Starbase 11 after First Officer Spock reports receiving a subspace call from Christopher Pike, the Enterprise's former captain, with whom Spock previously served. Captain Kirk and Spock meet Commodore Mendez, the starbase commander, who informs them that the severely disabled Pike couldn't have sent the message, as he can only communicate through brainwave-operated yes/no responses. Pike only agrees to communicate with Spock. When Kirk and Mendez leave, Spock reveals his plan to Pike, despite Pike's objections.

Mendez confirms no record of a message sent to the Enterprise and shares classified information about Talos IV, a quarantined planet visited by the Enterprise under Pike's command in 2254. Spock hijacks the Enterprise, places Pike under Dr. McCoy's care, and sets the ship's course for Talos IV. Kirk and Mendez pursue a Starbase shuttlecraft, but Spock eventually brings them aboard when fuel runs low.

Confessing to mutiny, Spock surrenders and admits the Enterprise is heading towards Talos IV. Mendez organizes a hearing, with Spock requesting an immediate court-martial requiring three command officers. Kirk objects, but Spock points out that Pike is still listed for active duty. The tribunal begins, and Spock presents video footage of the Enterprise's 2254 visit to Talos IV as evidence.

The footage shows the Enterprise arriving at Talos IV, responding to a distress call from the lost survey ship Columbia. Pike, Spock, and a landing party beam down to the planet and encounter survivors, including a young woman named Vina. Despite their situation, they are in perfect health. Vina reveals their secret to Pike, but he is then abducted by the Talosians, aliens with the power to create illusions indistinguishable from reality.

Back in 2267, a message from Starfleet Command interrupts the footage, revealing the images are transmitted from Talos IV. Mendez assumes command of the Enterprise, but Spock begs Kirk to watch the rest of the transmission.