09/20/68 -- Stardate: 5431.4
A young woman appears on the Enterprise bridge, kidnaps Spock, and takes him to her home planet, where his brain is removed in order to run the controls used to keep the planet's 10,000 year old machinery operating.
The Enterprise Incident
09/27/68 -- Stardate: 5031.3
Kirk, in Romulan disguise, and Spock play spies as they try to steal the cloaking device from a Romulan ship commanded by a proud female captain.
The Paradise Syndrome
10/04/68 -- Stardate: 4842.6
While trying to alter the path of an asteroid on a collision course with a planet containing a culture similar to that of the American Indians, Kirk suffers amnesia and marries one of the planet's young women.
And the Children Shall Lead
10/11/68 -- Stardate: 5029.5
The Enterprise crew finds that all of the adults on a distant colony have died and the children seem completely unconcerned, but later learn that a noncorporeal being called Gorgan has been controlling their minds.
Is There in Truth No Beauty?
10/18/68 -- Stardate: 5630.7
A blind telepath named Miranda Jones comes aboard the Enterprise with a Medusan ambassador, the sight of whom can make anyone, even the curious Spock, insane.
Spectre of the Gun
10/25/68 -- Stardate: 4385.3
When the Enterprise enters an uncharted sector of the galaxy, the bridge crew is transported to a deserted planet by unknown aliens and forced to play the part of the losing gunfighters in the gunfight at the O.K. Corral.
Day of the Dove
11/01/68 -- Stardate: Unknown
An alien creature that survives on the hatred of others manipulates the crews of the Enterprise and a Klingon cruiser into bloody hand-to-hand combat, but Kirk and the Klingon commander refuse to go along.
For the World Is Hollow and I Have Touched the Sky
11/08/68 -- Stardate: 5476.3
The Enterprise goes to investigate an asteroid on a collision course with a Federation planet, and discovers that the asteroid is really a hollow sleeper ship where generations of inhabitants have been travelling to a new home planet.
The Tholian Web
11/15/68 -- Stardate: 5693.4
While searching for the missing starship Defiant, the Enterprise is trapped in a force field web constructed by a Tholian ship, and Kirk is trapped in a rip in space between two alternate universes.
11/22/68 -- Stardate: 5784.0
After answering a false distress call, the Enterprise crew is held against their wills on a planet ruled by aliens with psychokinetic powers until the aliens' dwarf jester helps the crew members to escape.
Wink of an Eye
11/29/68 -- Stardate: 5710.5
Kirk is kidnapped by the Scalosians, a race with a highly-accelerated metabolic rate, to be bred to Scalosian women in an attempt to save the planet's dying population.
12/06/68 -- Stardate: 5121.0
Kirk, Spock, and McCoy are trapped on a planet where they are used by a race of advanced aliens to test the level of compassion of a mute empath named Gem.
Elaan of Troyius
12/20/68 -- Stardate: 4372.5
The Enterprise must transport a spoiled brat princess of the planet Troyius to the site of her politically-motivated marriage to an official of her planet's former enemies.
Whom Gods Destroy
01/03/69 -- Stardate: 5718.3
Kirk and Spock are captured by escaped lunatics in an asylum on Elba II, who try to trick Kirk into beaming them aboard the Enterprise.
Let That Be Your Last Battlefield
01/10/69 -- Stardate: 5730.2
In trying to recover a stolen shuttlecraft, the Enterprise is caught in the middle of the personal battle of the last two survivors of the planet Cheron, one of whom is white on the left side and black on the right, while the other is black on the left side and white on the right.
The Mark of Gideon
01/17/69 -- Stardate: 5423.4
When he attempts to transport down to the planet Gideon, Kirk finds himself aboard a completely deserted Enterprise, and later discovers that he is inside a replica on Gideon, a planet suffering from acute overpopulation.
That Which Survives
01/24/69 -- Stardate: Unknown
A beautiful woman who appears on the Enterprise kills a crewman with her touch, and the Enterprise crew later learns that she is an automated sentry of a long-dead race.
The Lights of Zetar
01/31/69 -- Stardate: 5725.3
Enroute to Memory Alpha, the Federation's central library facility, the body of Lt. Mira Romaine is invaded by a creature of pulsating lights that wants to continue to live in her body.
Requiem for Methuselah
02/14/69 -- Stardate: 5843.7
In search of the antidote for Rigellian fever, the Enterprise encounters a man named Flint and his female companion, and learn that Flint is a fluke of nature who has lived for thousands of years and was really also Brahm, da Vinci, and other famous artists of the past.
The Way to Eden
02/21/69 -- Stardate: 5832.3
When it tracks down a stolen ship, the Enterprise finds a band of space hippies who have their minds set on reaching the mythical planet Eden, even if it means hijacking the Enterprise.
02/28/69 -- Stardate: 5818.4
When the Enterprise goes to the planet Ardana for zenite, a substance needed to combat a botanical plague, the crew find themselves in the middle of a conflict between the ruling class, who live in a city in the clouds, and the working class, who live in underground caverns.
The Savage Curtain
03/07/69 -- Stardate: 5906.4
While investigating an uncharted planet, Kirk and Spock are transported by an unknown entity to the planet in the company of Abraham Lincoln and Vulcan's Surak to battle four evil counterparts from history.
All Our Yesterdays
03/14/69 -- Stardate: 5943.7
When the Enterprise goes to rescue any survivors of Sarpeidon, whose sun is about to go nova, Kirk, Spock, and McCoy inadvertently pass through a time portal and become trapped in different time periods of the planet's past.
06/03/69 -- Stardate: 5298.5
Janice Lester, a former Starfleet Academy rival of Kirk, executes a plan to switch bodies with him and take over as captain of the Enterprise.