- The Cage
- Where No Man Has Gone Before
- The Corbomite Maneuver
- Mudd's Women
- The Enemy Within
- The Man Trap
- The Naked Time
- Charlie X
- Balance of Terror
A Romulan Bird of Prey attacks the Federation outposts near the Neutral Zone, starting a cat-and-mouse confrontation with the Enterprise.
- What Are Little Girls Made Of?
In search of exobiologist Dr. Roger Kirby, Nurse Chapel's ex-fiancee, the Enterprise finds that he has constructed androids and given himself an android body in a plan to replace key Federation leaders with android duplicates.
- Dagger of the Mind
A maniac who escapes from the Tantalus 5 penal colony uses a brainwashing device in an attempt to gain control of the Enterprise.
The Enterprise encounters an Earth-like planet where a virus has killed all of the adults by causing them to age rapidly, while the aging process in children is slowed.
- The Conscience of the King
The Enterprise crew discovers that the leader of a traveling theater group is really Kodos the Executioner, who murdered most of the population of Tarsus 4 20 years earlier.
- The Galileo Seven
The shuttlecraft Galileo and its seven occupants crash-land on a hostile planet, and Spock must assume command to give them a chance at being rescued.
- Court Martial
Kirk is charged with negligence in the death of an Enterprise crewman, but is later acquitted when Spock discovers that the crewman isn't really dead.
- The Menagerie, Part 1
Spock commandeers the Enterprise to take Captain Christopher Pike to the off-limits planet Talos 4.
- The Menagerie, Part 2
Enroute to Talos 4 with Captain Pike, Spock faces a court-martial, during which the story of the first contact with the Talosians is revealed.
- Shore Leave
The Enterprise crew takes shore leave on a planet where their thoughts are brought to life by underground machinery of an advanced race.
- The Squire of Gothos
Four Enterprise crew members are kidnapped by Trelane, an arrogant, impetuous alien who turns out to be a child using the crew members as play things.
After chasing a Gorn ship into an uncharted sector of space, Kirk and the Gorn commander are transported to a desert planet, where they are forced to duel to the death.
- The Alternative Factor
The Enterprise finds Lazarus on a deserted planet, and soon discovers that he is in a life-and-death struggle with an evil duplicate from a parallel anti-matter universe.
- Tomorrow Is Yesterday
The Enterprise is thrown back in time to 20th Century Earth after a close encounter with a black star, and is reported as a UFO by an Air Force pilot.
- The Return of the Archons
The Enterprise crew beams down to a planet where the zombie-like inhabitants are controlled by a super computer known as Landru.
- A Taste of Armageddon
After the Enterprise is declared a victim of an interplanetary war fought only in the memory banks of opposing computers, Kirk and Spock force the warring planets to face the destruction of real war or settle their dispute.
- Space Seed
The Enterprise finds the SS Botany Bay, a 1990's sleeper ship carrying a group of genetically bred supermen led by Khan Noonian Singh.
- This Side of Paradise
All of the Enterprise crew, except Captain Kirk, are exposed to spores that induce a feeling of euphoria and a desire to remain on the planet.
- The Devil in the Dark
A mining colony on Janus 6 is faced with death and destruction caused by a rock-like creature, the Horta, which turns out to be a mother trying to protect her eggs from the miners' equipment.
- Errand of Mercy
The Organians intervene in a conflict between the Federation and the Klingons by imposing a peace treaty that will be enforced by the power of the Organians' minds.
- The City on the Edge of Forever
After an accidental overdose of the stimulant cordrazine, Dr. McCoy jumps through a time portal on a deserted planet and ends up on Earth in the 1930's.
- Operation - Annihilate!
While investigating the death of Kirk's brother and other colonists on Deneva, Spock is attacked by a flying creature that attaches itself to its victim's nervous system.