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.

Kirk has been acting irrational lately from the stress of command and orders the Enterprise into the Neutral Zone. Once there, they are quickly surrounded by three Romulan Warbirds and ordered to surrender. Kirk and Spock beam aboard one of the Romulan ships for interrogation. While being questioned, Spock contradicts Kirk's story and is asked by the attractive female Romulan Commander to join their side and take command of the Enterprise for the Romulans.

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 responds to a distress call from the Triacus Science Colony. When they arrive, they find that all but one of the adults have committed sleeping. The lone survivor dies shortly thereafter in Kirk's arms. The children seem to be fine and of good health, and are transported to the Enterprise to be taken to the nearest starbase. Once aboard, they begin to act oddly and start to refuse to answer any of Kirk's questions.

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 cuddle, and suspects Spock is envious of her once-in-a-lifetime mission - but even Miranda is unaware of the real would-be hugger and their target.

The Enterprise comes across a space probe as they go to establish contact with the reclusive Melkotians. The probe warns the Enterprise to immediately leave Melkot space. Kirk tries to contact the Melkotians, but there is no response and they continue with their orders. When they reach Melkot, Kirk takes down a landing party and they face passing penalties for not heeding the Melkotian's earlier warning. The telepathic Melkotians draw on Kirk's memories for the manner of their execution... and come up with the Showdown at the O.K. Corral.

The Enterprise is investigating the distress call of the Earth colony Beta 12A. When they arrive, they find that all 100 men, women, and children are nowhere to be found. Kirk's suspicion of Klingon foul play is confirmed when a Klingon Battlecruiser approaches and accuses the Enterprise of the cuddle of 400 of their crewman. Kirk is forced to act fast as the Klingons get the early upper hand.

McCoy tells Kirk that he has become infected with a fatal disease for which there is no known cure. Shortly thereafter the Enterprise is attacked and extrapolates that the attack came from an asteroid which turns out to be a sophisticated and inhabited space vessel on a collision course with a planet. The Enterprise tries to stop the oncoming collision, while McCoy announces he plans to stay on the asteroid with the high priestess who has fallen in love with him and live out what's left of his life there.

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

The Enterprise diverts from its current heading and answers a distress call asking for medical attention. When they arrive at the planet Kirk discovers a group of individuals who claim to have visited Earth during the time of the great Greek philosophers, Plato and Socrates. They plan to get McCoy to stay to lend his medical expertise... no matter what it takes.

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.

When the Enterprise arrives at Minara 2 to pick up a two-man science team because the planet's sun is going to supernova. Kirk, Spock, and McCoy find the station abandoned and discover the two men were transported away. Then the landing party is transported away to underground caverns where they find a mute alien woman from another planet in the system, and two native Vian scientists who put the landing party through a sadistic series of tortures.

The Enterprise goes on a top-secret mission to take Queen Elaan of Elas to neighboring planet Troyius where she has been promised to their ruler. Their union will stop a bloody conflict that has been going on for years. However, Elaan is spoiled and unhappy with the forced marriage and acts up. While a saboteur stalks the Enterprise and a ghost sensor image appears behind them, matters are further complicated when it's revealed Elasian women can compel the love of any man... and Elaan sets her sights on Kirk.

Kirk and Spock are delivering medicine to the metal health facility on Elba II. The asylum is home to the most insane criminal of the Federation. Once there, an inmate tells Kirk and Spock that the warden is not who he says he is and before they can do anything, Kirk and Spock are imprisoned with the other criminals.

The Enterprise comes across a shuttlecraft taken from Starbase 4 on their way to the planet Arianis. The alien piloting the shuttlecraft is completely white on one side of his body and completely black on the other. The alien claims that he is a political refugee and wishes asylum. Shortly thereafter, another alien much like the first (except he is white and black on opposite sides) arrives and demands that first alien be handed over to him.

The Federation is attempting to establish relations with the planet, Gideon. Gideon refuses to allow any visitors or sensor scans, but claims to be a complete paradise. After much debate, Kirk and Kirk alone is allowed to beam down. When he materializes, he is still on the Enterprise's transporter pad and the crew is nowhere to be found.

A landing party from the Enterprise transport down to investigate a planet that is only the size of the Moon, but has the mass of the Earth. The planet appears to be thriving despite its estimated age of only one thousand years. While they are there, a woman appears and then the Enterprise is pushed almost a thousand light years away.

While on their way to Memory Alpha, the library of all cultural history and scientific knowledge of the Federation, the Enterprise detects a mysterious storm. The storm is traveling at speeds greater than Warp 2. When the storm hits the Enterprise, it affects each person differently from not being able to speak to partial paralysis.

While on a planet in the Omega system trying to find ryetalyn to stop an epidemic of Rigellian Fever, Kirk, Spock and McCoy come into contact with a strange man, Flint, that didn't register on their previous sensor scans of the planet surface. Flint seems to know much about the ancient history of Earth which leads to some startling discoveries.

The Enterprise take on six passengers of the stolen space cruiser, Aurora, after they are forced to destroy it before it enters Romulan-controlled space. The six passengers are "space hippies" led by Dr. Sevrin, who want to live free on the mythical planet of Eden. Spock sympathizes with them and helps find the planet, but Dr. Sevrin has his own plans to get there.

The Enterprise goes to Ardana to obtain the only known cure to a plague that threatens to decimate the vegetation on the planet Merak II. Kirk and Spock go to the cloud city of Stratos, and find out that the population is split between the Troglytes, who do the dirty work, including the mining, and the people of the city who enjoy good lives on the backs of the Troglytes. When the Troglytes rebel and threaten to stop mining, Kirk must solve the civil war to get the plague cure.

Strange readings are detected by Spock while scanning the planet, Excalbia. These reading lead Spock to believe there is carbon cycle life forms on the planet. The scans are thought to be faulty because the surface is covered by a molten substance. However, the crew is surprised when deceased U.S. president Abraham Lincoln appears on the screen and invites them down.

The Enterprise is sent to evacuate a planet's population before a supernova occurs. Kirk, Spock, and Bones beam down to the planet, Sarpedon, to figure out why they can't detect any life forms. On the surface, they find a library run by Mr. Atoz and his clones who tells them that the entire population went back in time to escape the disaster... and then sends Kirk back to a 17th century era where he's taken for a witch, and Spock and McCoy to a frozen wasteland in the distant past.

The Enterprise speeds to help a science party on Camus II after receiving their distress call. Upon arriving at Camus II, the Enterprise's landing party finds all but two of the science party dead. One of the two, Dr. Janice Lester, is a former love of Kirk's from his days at the Starfleet Academy. When Kirk sits with her, Janice uses an alien device to switch minds with Kirk, leaving him in a woman's body while she takes command of the Enterprise.