Enterprise encounters an ion storm, which requires an observer in the ion pod. Top of the duty roster is Commander Ben Finney, who is tragically lost when Kirk must eject the pod as part of the Red Alert protocol. At the starbase, Commodore Stone discovers that the computer records tell a different story: that Kirk ejected the ion pod during Yellow Alert, and that if he had waited properly, Finney might still be alive. He offers Kirk a chance to resign his commission "for the good of the service", but Kirk refuses - and so draws a general court martial. His advocate? The quirky Samuel Cogley, who eschews his computer in favor of books.

The Enterprise chances across a DY-100 class ship, launched from Earth "in the 1990s". It carries around seventy people, who have been hibernating since their launch. The ship's systems revive the leader, whom Kirk soon learns is Khan Noonien Singh, the leader of a group of genetically enhanced "supermen" who nearly took control of Earth during the Eugenics Wars. They have essentially fled to the future, and with their capabilities, Khan plans to revive his campaign to place "superior" men in positions of leadership.