This episode and the sequel are derived from the original pilot for the Star Trek series, The Cage. The Enterprise diverts to Starbase 11 after Spock reports receiving a sub-space message from former Captain of the Enterprise Christopher Pike. However, the Commodore on the Starbase tells them that Pike has been injured from exposure to delta rays (resulting from a ruptured baffle plate while inspecting an old Class J starship) and could not have sent the message. This is confirms when Pike wheels confined to a wheelchair which is operated by brain waves. The only communication of which Pike is still capable is signaling yes (one flash of a light) or no (two flashes). Pike refuses to speak to Bones or Kirk, but agrees to speak to Spock in private.
Spock, who had served under Pike for 11 years, 4 months, and 5 days, prepares to mutiny in order to take Pike to Talos 4 (the fourth planet out of 11 in the Talos system), despite Pike's protests. Meanwhile, an investigation of the tapes reveals that Spock received no transmission, but Kirk refuses to believe it possible that Spock could have been responsible for a deception. Spock nerve pinches Chief Humboldt at the computer center and sends the Enterprise bogus instructions using tapes he has made of Kirk's voice. Another technician discovers Spock cross-circuiting the communications panel and attempts to stop him, but is nerve pinched for his efforts. Spock informs Mr. Hansen that the coded transmissions he has sent will navigate the ship automatically. McCoy is tricked into returning to the Enterprise by a request for medical assistance. Spock then transports himself and Pike aboard.
Right After Miss Piper (who knows about Kirk from mutual fried Helen Johansen) glances at her closed-circuit monitor and notices that Pike is gone, the Enterprise warps out of orbit towards Talos 4. Kirk and Commodore José Mendez pursue Spock and the Enterprise in a Class F shuttlecraft. Aboard the Enterprise, Hanson is superfluous as navigator while the instructions Spock fed into the computer are carried out automatically. When Spock notices that the shuttlecraft has nearly exhausted its fuel, he activates tape Abel 7 Baker, which stops the Enterprise and beams aboard Kirk and Mendez. Spock then informs them that has set up the ship's computer so that it cannot be disengaged without terminating life support systems until the Enterprise reaches Talos 4.
Spock is then put on trial. Not only is mutiny a court martial offense, but visiting Talos 4 is an offense punishable by death. The hearing proceeds because Pike is still listed as on active duty, so three command officers are present as required by regulations. During the hearing, Spock introduces a recording of the experiences of the original crew of the Enterprise on Talos 4 as evidence.
In the tape we see footage from the original Star Trek pilot episode, The Cage. The tape recounts how 13 years previously the Enterprise, commanded by Pike and with Dr. Heinz as chief medical officer, received a distress signal from the survey vessel S.S. Columbia, lost 18 years earlier. The Columbia reported making a forced landing on the Talos star group 18 years ago. Mr. Spock (the only character from the original pilot retained in the original series except for Nurse Christine Chapel, who tool a huge demotion from ``Number One'') reports that Talos contains 11 planets, number 4 of which is Class M (oxygen atmosphere). Captain Christopher Pike orders to continue on to the Vega colony in the absence of evidence that there are survivors.
Pike then retires to his cabin, where he is met by Dr. Phil Heinz. Pike recounts his traumatic experience on Rigel 7 in which his yeoman and two others were killed and 7 injured. Pike faults himself for allowing himself to be trapped in a deserted fortress and attacked by one of the Rigel warriors. He also complains that he is tired of being responsible of 203 lives and has been thinking of resigning. However, he is quickly distracted from such thoughts when follow-up message from the Columbia indicates that 11 crew members survived the crash. Pike commands the Enterprise to divert and investigate.
Talos 4 is found to have an oxygen-nitrogen atmosphere and gravity equal to 0.9 that of Earth. On Talos 4, Spock and Pike find a blue-leaved plant, and we are treated to one of the few Spock smiles of the series (and the only one when he is not under some alien or hallucinagenic influence). The landing party of 6 finds survivors of the Columbia who are now old male scientists (including Dr. Theodore Hat of the American Continent Institute), but also a young woman named Vena who was born shortly after the Columbia crashed and whose parents are now dead.
Unbeknownst to the landing party, their actions are being monitored by native Talosians. The doctor notices that the condition of the survivors is better than could be reasonably expected, and becomes suspicious. Before he can find out what is going on, Vena leads Pike into a Talosian trap. As soon as Pike is drugged and captured by the Talosians, the survivors, who were illusionary, vanish. In a desperate attempt to rescue Pike, the landing party tries to blast through the rock into which Pike was spirited away, but their phasers have no effect.
At this juncture, Uhura reports that the Enterprise has been receiving transmissions from Talos 4 and Kirk is relieved from duty by order of the Starfleet Command Consul.