9/20/1968. Spock's Brain — A woman steals Spock's brain for use as a utilities regulator on her home world, leading the Enterprise crew on a mission to retrieve it.
9/27/1968. The Enterprise Incident — Kirk, behaving erratically, steers the Enterprise into the Romulan neutral zone, where he finds himself surrounded by Romulan vessels.
10/4/1968. The Paradise Syndrome — When Kirk awakens to find himself abandoned and suffering from amnesia on a simple, primitive world, he finds happiness and love with the native people, who accept him into their tribe.
10/11/1998. And the Children Shall Lead — A landing party beams down to a research colony to find the scientists dead, and their surviving children exhibiting no signs of grief.
10/18/1968. Is There In Truth No Beauty? — The Enterprise provides transport for an alien ambassador and his companion, a human telepath trained in Vulcan mind techniques.
10/25/1968. Spectre of the Gun — An alien death sentence places Kirk and his officers in a surrealistic recreation of a showdown in the Old American West.
11/1/1968. Day of the Dove — The Enterprise becomes a battle arena when Klingon prisoners aboard the Enterprise escape their confinement and an alien being incites each side into violent confrontations with the other.
11/8/1968. For the World Is Hollow and I Have Touched the Sky — Upon analyzing an asteroid on a planetary collision course, the Enterprise crew discovers the object is actually an advanced spaceship that, to its passengers, appears to be a world of its own.
11/15/1968. The Tholian Web — An investigation of the USS Defiant, found dead in space, results in Kirk being suspended in a spatial void—leaving Spock to face a confrontation with the Tholians as McCoy attempts to cure an outbreak of insanity crippling the crew.
11/22/1968. Plato's Stepchildren — When McCoy refuses to accept permanent duties among a community of people with telekinetic powers, their leader subjects members of the Enterprise crew to cruel humiliation.
11/29/1968. Wink of an Eye — Kirk is abducted to the realm of the Scalosians, who live their lives in a vastly accelerated time continuum.
12/6/1968. The Empath — Attempting to determine the whereabouts of a missing research colony, Kirk, Spock, and McCoy suddenly find themselves the pawns in a deadly alien experiment.
12/20/1968. Elaan of Troyius — A diplomatic mission places Kirk in the role of etiquette teacher for a warrior whose world needs her to make peace with its long-embittered neighbor.
1/3/1969. Whom Gods Destroy — While delivering medicine to a penal colony for the insane, Kirk and Spock are taken prisoner by a megalomaniac bent on unleashing his wrath upon the universe.
1/10/1969. Let That Be Your Last Battlefield — The Enterprise becomes the latest battleground for the millennia-spanning strife between two bitter enemies from a world paralyzed by racial hatred.
1/17/1969. The Mark of Gideon — Upon beaming down to the planet Gideon, Kirk finds himself on a duplicate of the Enterprise with a woman who yearns of a place where she can escape the extreme overpopulation of her home world.
1/24/1969. That Which Survives — A landing party must solve the mystery of a woman who is the cause of several crew members' deaths and the sabotage of the ship's engines.
1/31/1969. The Lights of Zetar — Scotty falls for a woman who becomes the latest target of a non-corporeal alien presence in need of a human form.
2/14/1969. Requiem for Methuselah — While searching for a needed medicine to combat a plague, the Enterprise landing party encounters a social recluse who had long ago abandoned Earth and now lives alone with his enigmatic pupil.
2/21/1969. The Way to Edenzero stars — A group of non-conformists takes control of the Enterprise and sets it on a course for the mythical planet of Eden.
2/28/1969. The Cloud Minders — While attempting to obtain a crucial mineral to cure a planetary plague, Kirk is drawn into the struggle of a world divided by class exploitation.
3/7/1969. The Savage Curtain — An entity claiming to be Abraham Lincoln invites Kirk and Spock to the planet surface, where an advanced lifeform vies to study the methodologies of both good and evil.
3/14/1969. All Our Yesterdays — The landing party investigates the final hours of a planet whose star is going supernova, and whose people have escaped the coming death of their world by traveling into their society's past.
6/3/1969. Turnabout Intruder — One of Kirk's former lovers, consumed with jealousy and bitterness for being denied a Starfleet captaincy, renders Kirk unconscious and trades bodies with him, assuming his identity and abusing the powers of his command.