Suffering through the pon farr, the Vulcan biological mating urge, Spock must return to Vulcan to marry his betrothed or he will die. However, when the Enterprise arrives at Vulcan, complications at the ceremony may endanger Captain Kirk as well.

The Enterprise is held captive within an energy field which is controlled by an alien who claims to be the Greek god Apollo. Apollo commands Kirk to meet him on the planet's surface. Bones, Chekov, Scotty, and Lieutenant Carolyn Palamis accompany Kirk. Apollo demands the crew worship him as a god at his temple, captivating Carolyn and attacking Scotty when he disobeys. Spock finds a way to get through the energy field and helps Kirk to take down the temple that was the power source of the energy field.

Nomad, a powerful reconstructed artificially intelligent Earth probe with a murderously twisted imperative comes on to the Enterprise and confuses Capt. Kirk as his creator.

Beamed up during an ion storm, which causes a transporter malfunction, the landing party of Kirk, McCoy, Scotty and Uhura find themselves in a mirror universe aboard a parallel Enterprise run by ruthless barbarians. The ion storm also caused their malicious counterparts to beam to the real starship. Kirk and the others must find a way home before they are discovered and exposed by their parallel crew members, who use treachery, back-stabbing and seduction to get what they want.

Kirk and a landing party beam down to what seems to be an ideal, Eden-like planet. They soon find however that the planet is ruled by a powerful computer that keeps its local inhabitants - primitive and simple tribesmen - happy and healthy. With the Enterprise locked in a tractor beam and slowly being dragged into the planet's atmosphere, Kirk and Spock must find a way to disable to computer. Realizing the threat to its existence, the computer orders the tribesmen to kill the visitors.

The USS Enterprise encounters the wrecked USS Constellation and its distraught captain determined to stop the giant planet destroying robot ship that killed his crew.

When Kirk and his landing party arrive on the planet below, they are met by eerie mists, a dark castle, witches, goblins and a black cat. They soon learn that they are under the influence of a wizard, Korob, who tries to bend them to his will. They also soon learn that the black cat they saw is more than she appears and is in fact a powerful witch in her right. It is left to Kirk and Spock to find a means to escape their grasp.

Harry Mudd returns with a plot to take over the Enterprise by stranding the crew on a planet populated by androids under his command.

The Enterprise, carrying a critically ill Federation Ambassador Nancy Hedford, encounter a mysterious energy cloud which pulls them down to planet Gamma Canaris N, where they meet a castaway. This young man purports to be Zefram Cochrane, the inventor of the Warp Drive over 100 years ago. But in history he had lived to be 80 years of age before disappearing somewhere in space. Apparently the same energy cloud which brought the Enterprise to the planet also rejuvenated Cochrane, making him effectively immortal. Can Kirk get the Enterprise released on time to get the ambassador the medical help she needs, or is there something else in this situation which might be a solution?

The Enterprise hosts a number of quarrelling diplomats, including Spock's father, but someone on board has murder in mind.

The Federation is in competition with the Klingons for an alliance with the inhabitants of Capella IV. The Capellans are a warrior tribe and there is dissension among them as to who to sign the mining rights treaty with. McCoy is familiar with their customs having once spent several months there. When a Capellan, who clearly favors the Klingons, stages a coup, Kirk, Spock and McCoy flee with the now dead leader's wife, who is about to give birth. Meanwhile, the Enterprise receives a distress call from a Federation vessel under attack and, with Scotty in command, leaves orbit.

A landing party from the Enterprise is exposed to strange form of radiation which rapidly ages them.

Capt. Kirk obsessively hunts for a mysterious cloud creature he encountered in his youth.

Kirk and the Enterprise Computer become detectives after Scotty is accused of murdering women on a pleasure planet.

To protect a space station with a vital grain shipment, Kirk must deal with Federation bureaucrats, a Klingon battle cruiser and a peddler who sells furry, purring, hungry little creatures as pets.

Kirk, Uhura and Chekhov are trapped on a planet where gladiators are enslaved and trained to perform for the amusement of bored, faceless aliens.

The Enterprise is investigating a planet visited 100 years ago by the USS Horizon. Kirk, Spock, and McCoy beam down and find themselves in a culture similar to Earth gangs of the 1920's. They are quickly taken prisoner by men in the employ of a mob boss named Bela Oxmyx. He wishes them to give him phasers in exchange for "a piece of the action", and when they refuse Oxmyx puts them under guard. Kirk creates a diversion with a card game called "fizzbin". Without their equipment, the trio must find a way to unite the planet and escape to the Enterprise.

The Enterprise encounters a gigantic energy draining space organism that threatens the galaxy.

Kirk returns to the planet Neural which he had spent time 13 years before. A friend of his from his previous visit is now leader of his people. While trying to uphold the Federation's prime directive, the Klingons are providing more advanced technology to their enemies.

The last three members of an ancient race far more advanced than humans, who survive only as disembodied thought, wish to borrow the bodies of Kirk, Spock and Dr. Mulhall.

Looking for a missing Federation cultural observer, Kirk and Spock find themselves in a planet whose culture is now modeled on the German Nazi Party of old Earth in the 1930's.

Galactic alien scouts capture the Enterprise for a return voyage and a prelude to invasion. Kirk's one advantage - they're not used to their adopted human form.

Responding to a distress signal, Kirk finds Captain Tracey of the USS Exeter violating the prime directive and interfering with a war between the Yangs and the Kohms to find the secret of their longevity.

Kirk and a sub-skeleton crew are ordered to test out an advanced artificially intelligent control system that could potentially render them all redundant.

While searching for the crew of a destroyed spaceship, the Enterprise discovers a planet whose oppressive government is a 20th-century version of Earth's Roman empire. Kirk, Spock, and McCoy meet the rebels, seemingly sun worshipers, but are quickly kidnapped by the regime. The missing Captain Merrick is revealed as the "First Citizen" and pawn of the regime, but he and the rebels ultimately help Kirk and company to escape. Back on the Enterprise, Uhura observes that the crew's understanding that the rebels are sun worshipers was not completely accurate.

The Enterprise travels back in time to 1968, where the crew encounters the mysterious Gary Seven who claims to be sent by advanced beings trying to help Earth.