Kirk and Spock are taken prisoners by a former starship captain named Garth, who now resides at, and has taken over, a high security asylum for the criminally insane.
Kirk beams down to the planet Gideon and appears to find himself trapped on a deserted Enterprise. Spock on the real Enterprise must use his diplomatic skills to deal with the uncooperative inhabitants of Gideon and find the Captain.
After the Enterprise landing party beams down to investigate a geologically interesting planet, their ship is hurled across the galaxy. Kirk and company find a deserted outpost guarded by the deadly image of a beautiful woman.
On a planet, looking for an urgent medicinal cure, Kirk, Spock and McCoy come across a dignified recluse living privately but in splendor with his sheltered ward and a very protective robot servant.
Kirk and Spock are caught up in a revolution on a planet where intellectuals and artists live on a utopian city in the sky while the rest of the population toils in mines on the barren surface below.
Kirk, Spock, Abraham Lincoln and Vulcan legend Surak are pitted in battle against notorious villains from history for the purpose of helping a conscious rock creature's understanding of a concept he does not understand, "good vs. evil".
When Kirk, Spock and McCoy investigate the disappearance of a doomed planet's population, they find themselves trapped in different periods of that world's past.