While exploring on the outer most rim of the galaxy the Enterprise is pulled into the orbit of a dead star. Trapped there, they discover an ancient derelict pod ship also trapped in the orbit. When they investigate they find that the pod ships crew destroyed their own craft, to keep it from being used by an alien entity, which needs a warp drive to escape the dead sun. When it beams aboard the Enterprise, Kirk must find a way to get rid of it, without destroying his ship in the process.
Mr. Spock returns from a time-traveling research project to find that no one onboard the Enterprise remembers him. Now he must go back through the time gate to his Vulcan childhood, and save the life of the child he was. The many complicated issues explored in this story raise it far above the standard Saturday morning fare.
A giant planet eating cloud is heading for Mantilles, home to a Federation colony. Kirk takes the Enterprise inside the cloud in an attempt to stop it. However once inside, the ship loses power and Spock realizes the cloud is an intelligent being.
The Enterprise enters a sector of space where vessels have been reported missing every 27 years. While in the Taurean system signals begin to affect the male crew, causing them to hallucinate. Kirk, Spock, and McCoy beam down to the source of the signals. After arriving on the planet they are taken prisoner by a group of beautiful women. The landing party begins to age rapidly as a result of life-draining headbands they are forced to wear. On board the Enterprise, Uhura has taken command due to Scotty's irrational behavior. Uhura orders an all-female landing party to transport down to rescue the men. The landing party eventually beams the male landing party back up to the ship just in time to replenish their life-force.
While the Enterprise is escorting two robot ships loaded with Quintrotriticale, a new seed grain for famine stricken Shermans planet, it encounters a Klingon battlecruiser in pursuit of a Federation scout ship. The Klingons attack the Enterprise with a new energy weapon when it rescues the pilot. Cyrano Jones, proud owner of the Glommer, and the intergalactic trader the Klingons desperately want, is now selling Tribbles that don't reproduce, they just get bigger!!
Near the Romulan/Federation neutral zone, a long-lost philanthropist, Carter Winston, is discovered on board a damaged one-man vessel. But, Winston is actually a shape-shifting Vendorian, who, takes the Captain's form and orders Sulu to steer the Enterprise into the Neutral Zone, where Romulan warbirds lie in ambush!
While visiting the newly discovered planet Phylos, Sulu picks up a walking plant, called a Retlaw (Walter spelled backwards), and is poisoned. The alien species that inhabit the planet, who are plantlike beings, approach and save Sulu's life. From them the crew discovers that most of the Phylosians were wiped out by a plague brought to the planet by a Terran scientist named Dr. Starros Keniclius. A giant clone of Keniclius, named Keniclius Five, kidnaps Mr. Spock in order to clone him and create an intergalactic peacemaker, at the expense of the original Spocks life.
Exploring the center of the galaxy, the very heart of creation, the Enterprise is caught inside an energy/matter tornado and all computer systems fail. A being named Lucien appears on the bridge, repairs the ship's systems and takes the crew to explore his planet, Megas-Tu. On this planet, what we would consider to be magic is normal. The Megans are an ageless species that had, at one time, lived on Earth, and were responsible for the legends about witches. They decide to put Kirk and crew on trial for the crimes of mankind.
The crew revisits the amusement planet first seen in the TOS episode "Shore Leave". This time the robots the planet produces are aggresive, and dangerous. Lt. Uhura is captured by the planets master computer, who in the wake of the "Keepers" death, resents being made to serve humans.
The U.S.S. Enterprise receives orders to arrest Federation outlaw Harry Mudd, who is accused of selling a fake love potion. Aboard the Enterprise, and after convincing Nurse Chapel to try the potion on Spock, Mudd steals a shuttlecraft. During a struggle some of his love crystals are accidentally broken near an air vent affecting the entire crew.
While observing a burnt-out supernova, the Enterprise picks up a strange message transmitted in a 200 year old code. The signal is traced to a nearby planet, and when the ship arrives it is hit by an energy beam that damages it's dilithium crystals, and makes the crew begin to shrink. Dr. McCoy discovers that the crew will continue to shrink beyond their ability to control the ship unless a cure is found.
While exploring the Delta Triangle, where many starships have disappeared, the Enterprise is attacked by several Klingon vessels. During the fight, the Enterprise and a Klingon ship slip into a space-timewarp starship graveyard. The crew discovers that the timewarp is disintegrating the Enterprise's dilithium crystals, and that they must link their ship with the Klingons to leave the trap, or they will be powerless and trapped forever.
While exploring the water planet Argo, Captain Kirk and Mr. Spock are transformed into water breathers by the planets inhabitants, the Aquans. In order to return to their normal human selves, they must enlist the help of the Aquans to capture a giant sur-snake, whose venom holds the antidote.
In the shuttlecraft Copernicus, Spock, Uhura, and Sulu are en-route to Starbase 25 to deliver a stasis box -- a rare artifact of the Slaver culture. The now-extinct Slavers used these objects to carry weapons, valuables, and other scientific instruments and data. The boxes can detect each other and evidence shows that another device is located nearby. The shuttle lands on an ice planet where hostile Kzinti lie in ambush.
The disappearance of a scientific team lures the U.S.S. Enterprise to investigate near Lactra VII. The Starship Ariel is located there, abandoned, with the Captain having transported to the planet's surface. The U.S.S. Enterprise crew beams down to discover a series of unusual environments. On the planet the crew meets the Lactrans, a group of twenty foot slugs with intelligent capacities far beyond their own.
The U.S.S. Enterprise arrives at the Vedala asteroid, where Kirk and Spock are summoned to learn about a stolen religious artifact, the "Soul of the Skorr", whose theft could ignite a galaxy-wide holy war, a jihad. Joining Kirk and Spock are a team of specialists called in to help recover the item, which has been hidden on a very unstable "mad planet", Tchar -- the hereditary prince of the Skorr, Sord -- a powerful reptilian, Em/3/Green -- a master lockpick , and Lara -- a great hunter.
The Enterprise is on it's way to Deneb 5 when Mr. Spock contracts choriocytosis and has only days to live. The USS Huron is to rendezvous with the Enterprise and deliver the cure, when it's attacked by the Pirates of Orion. Kirk chases the Orion ship in a desperate attempt to save Spocks life.
The Enterprise is being visited by the Pandronian commander Ari Bn Bem, who is an independent observer. He accompanies a landing party on a mission to a newly discovered planet, but, instead of observing, he interferes with the mission. Before long, Kirk and his people are captured. Then they encounter a powerful alien entity who insists they leave the planet.
When the Enterprise is attacked by three Romulan warbirds, it hides in a gaseous energy field. The cloud affects the computer and it begins to play practical jokes on the crew, like making glasses leak, silverware turn to rubber, and covering decks with ice. The highlight of this episode is when McCoy, Uhura, and Sulu get trapped in trekdoms very first malfunctioning holodeck. The insurance rates for those things must be murder!
When the Enterprise visits Dramia to deliver medical supplies, the authorities arrest Dr. McCoy for mass murder. They contend that 19 years earlier McCoy had supervised an inoculation program on Dramia II, and that once he had left most of the inhabitants died from a plague. Kirk takes the Enterprise to Dramia II to investigate, and the crew gets infected with the same plague.
Following the signal of a mysterious probe, the Enterprise is immobilized by an alien whose ship resembles a winged serpent, and who claims to be Kukulkan the ancient god of the Mayan-Aztec people on Earth. Kukulkan transports Kirk, McCoy, Scotty, and Walking Bear to his ship, where they find an ancient city, and are told they must solve the puzzle of the city or the Enterprise will be destroyed.
The Enterprise is taking it's first Captain, Commodore Robert April, and his wife, Sarah, to Babel, when it sees a ship flying into a super nova. The Enterprise tries to help by locking a tractor beam onto it, but is pulled into a negative universe where time flows backwards. The pilot of the alien ship agrees to help them get back, but the crew is rapidly growing younger and will soon be unable to operate the ship.