Stardate 5431.4: The Enterprise is intercepted by a starship of unknown design and a woman from the ship beams directly into the bridge and uses a device to render the Enterprise's crew unconscious. She then walks over to Spock... When the crew awakens, McCoy summons Kirk to sick bay and informs him that the alien visitor apparently removed Spock's entire brain without even performing surgery. After Spock's body is fitted with a device that allows McCoy to control the Vulcan's motor functions with a remote control, Kirk starts a search for Spock's brain, hoping it can be recovered and somehow returned to Spock before his body decays.

An unusually tense and irritable Kirk orders his ship into the Romulan Neutral Zone, where it is promptly surrounded. Beamed to a Romulan ship, Kirk lies about the intrusion, then attacks Spock, who responds with a Vulcan death grip. While the female Romulan commander courts Spock, a secret mission unfolds.

Stardate 4842.6: Kirk, Spock and McCoy beam down to a planet to inform any inhabitants that they must evacuate the planet due to an approaching asteroid's imminent collision. A society similar to Native American Indians has arisen on the planet, but near their villages, the landing party finds a strange obelisk whose design and construction is far beyond the capabilities of the planet's natives. Kirk finds that the monolith can be opened by the combination of sounds found in the order ""Kirk to Enterprise,"" but when he enters the obelisk, he is attacked by waves of energy that erase his mind. With no time to spare, Spock and McCoy have to return to the Enterprise without Kirk, and begin trying to use the ship's tractor beam to divert the asteroid. Meanwhile, Kirk becomes the tribal chief, takes a wife and even expects to become a father, but the Enterprise may not be able to save her former captain's future.

The Enterprise travels to a planet where a scientific team has killed themselves...except for the children, who began to act oddly.

Stardate 5630.7:...or is there in beauty no truth? Miranda Jones, a telepath who studied mental disciplines on Vulcan, arrives with Ambassador Kolos, a Medusan - an alien life form whose physical form is so hideous, humanoid life forms are driven insane if they look upon him. Also beaming aboard is Larry Marvick, one of the original designers of the Enterprise - and hopelessly in love with Miranda, although she has chosen to spend her life serving as a liason between the Medusans and other humanoids. Miranda senses that someone is actively contemplating murder, and suspects Spock is envious of her once-in-a-lifetime mission - but even Miranda is unaware of the real would-be killer and their target.

When coming to an exaphobic isolationist planet, Captain Kirk and his landing party are punished for trepassing. They are sentenced to death in a surreal recreation of the Gunfight at the OK Corral with the landing on the losing side.

When the Enterprise brings aboard Klingon prisoners, an alien entity pits both sides against each other in an ever-escalating struggle.

The Enterprise must deflect an asteroid on a collision course with an inhabited planet...but discover the asteroid is a spaceship with a population unaware of the outside world.

Stardate 5693.2: The Enterprise arrives at the last known position of the U.S.S. Defiant (NCC-1764), an area of uncharted space, to search for the missing starship. When the Defiant appears on the viewing screen enshrouded in a strange green glow, Spock is unable to scan the vessel on his sensors. Kirk beams over to the Defiant with a boarding party to investigate and finds the entire crew dead. What's more, the Defiant seems to be trapped in an interphase between two different universes. A power loss partially disables the Enterprise transporter, but the landing party manages to beam back to the Enterprise except Kirk who suddenly disappears along with the Defiant. Spock calculates that the next time to interphase will be approximately two hours, and that the captain can be rescued at that time. As the Enterprise begins to experience the same problems that doomed the Defiant: power loss, weakness and insanity among the crew, an alien vessel appears and demands that they leave Tholian

Kirk and his crew find themselves at the mercy of powerful individuals who possess mind-over-matter powers...and plan to use the Enterprise crew for their twisted entertainment.

Stardate 5710.5: When a landing party investigating Scalos begins to vanish one by one, Kirk, Spock and McCoy try to find out what is happening before more of the crew disappears, until Kirk himself is abducted. Kirk finds the cause to be a group of endangered Scalosians who move faster than human sight or hearing can detect. They need to repopulate their species, and find that speeding human males up to Scalosian speed will meet their needs. Kirk must find a way to get a message to Spock and McCoy, who are working on a cure for the mystery ""ailment,"" as well as stirring up fighting among the Scalosians, before they have control of the Enterprise.

On a planet doomed to destruction, Kirk, Spock & McCoy become involved with two aliens who use them as laboratory animals in a bizarre series of tests on an alien empath who may be the savior of her planet.

The Enterprise must escort an alien princess to her marriage to seal an interplanetary alliance...but she becomes attracted to Kirk.

Kirk and Spock investigate an insane asylum where a former Starfleet captain is being held, only to discover that he has freed the inmates and is running the place.

The Enterprise finds itself host to two alien beings from the same planet, who share an intense and self-destructive hatred of each other.

Kirk beams down on a diplomatic mission...and finds himself in an Enterprise where all the crew have vanished and only a mysterious woman resides.

Kirk, McCoy, and Sulu are stranded on a barren planet where a mysterious woman attempts to kill them one at a time, while the Enterprise must travel halfway across the galaxy to rescue them.

The Enterprise must deal with discorporeal cloud-like corporeal aliens who have already destroyed the inhabitants of a library planet and plan to eliminate the Enterprise crew if they cannot acquire a human host.

While seeking a cure for a fever ravaging the Enterprise, Kirk and Spock encounter Flint, a hermit-like Earthman, and his beautiful young ward.

The Enterprise picks up a group of space ""hippies"" looking for Eden.

Kirk must resolve a mining dispute on a the cloud city of Stratos to acquire the resources to cure a space plague.

Kirk and Spock meet Abraham Lincoln and Surak of Vulcan and must do battle with some of histories most terrible villians.

Kirk, Spock, and McCoy become trapped in the past of another world.

The Enterprise is in danger when Janice Lester, one of Kirk's former lovers, steals his body.