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Season 1 - Episode 2 -- Charlie X

The Enterprise picks up an unstable teenage boy with dangerous mental powers.

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Season 1 - Episode 3 -- Where No Man Has Gone Before

The Enterprise journeys to the edge of the galaxy, where two crew members develop dangerous psychic powers.

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Season 1 - Episode 4 -- The Naked Time

A strange illness infects the crew of the Enterprise, causing them to live out their latent desires and fears.

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Season 1 - Episode 5 -- The Enemy Within

A transporter mishap divides Captain Kirk into separate beings, one gentle, the other evil.

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Season 1 - Episode 6 -- Mudd's Women

The Enterprise picks up a traveling con man, Harry Mudd, and his beautiful female "cargo"; the females seem to have a strange effect on the male crew.

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Season 1 - Episode 7 -- What Are Little Girls Made Of?

Nurse Chapel searches for her long lost fiancé, and uncovers his secret plan for galactic conquest.

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Season 1 - Episode 8 -- Miri

The Enterprise discovers an exact duplicate of Earth, where the only survivors of a deadly plague are the planet's prepubescent children.

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Season 1 - Episode 9 -- Dagger of the Mind

The Enterprise visits a prison planet where a new treatment for the criminally insane (a machine that affects their mind and memories) has deadly results.

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Season 1 - Episode 10 -- The Corbomite Maneuver

The Enterprise initially encounters a cube-shaped probe in space; further investigation reveals the probe's source (a massive starship with an unusual pilot).

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Season 1 - Episode 11 -- The Menagerie, Part I

Spock violates Federation standing orders by helping his former captain, Christopher Pike, return to the forbidden planet Talos IV.

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Season 1 - Episode 12 -- The Menagerie, Part II

Spock is put on trial for helping his former captain, Christopher Pike, return to Talos IV.

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Season 1 - Episode 13 -- The Conscience of the King

Captain Kirk crosses paths with an actor suspected of having been a murderous dictator many years before.

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Season 1 - Episode 15 -- Shore Leave

The crew of the Enterprise visits a bizarre planet of dangerous illusions, encountering the rabbit from "Alice in Wonderland", fighter planes and Samurai.

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Season 1 - Episode 16 -- The Galileo Seven

Mr. Spock commands a team aboard an Enterprise shuttlecraft that has crashed on the surface of an unexplored planet with aggressive humanoid creatures.

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Season 1 - Episode 18 -- Arena

After the colony on Cestus III is destroyed, the Enterprise pursues an alien ship into unknown territory. Both the ships are disabled by a mysterious force and Captain Kirk is forced to fight the lizard-like, alien captain of the other ship.

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Season 1 - Episode 19 -- Tomorrow Is Yesterday

The crew of the Enterprise travels back to 1960's Earth, and must correct damage they cause to the timeline.

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Season 1 - Episode 20 -- Court Martial

Captain Kirk stands trial on charges of negligence leading to the death of a crewman, and the Enterprise computer is the main witness against him.

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Season 1 - Episode 21 -- The Return of the Archons

The crew of the Enterprise encounters a world with a dysfunctional society controlled by an unseen leader.

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Season 1 - Episode 22 -- Space Seed

The Enterprise re-awakens a dangerous genetically-enhanced dictator from Earth's Eugenics Wars in the 1990s - Khan Noonien Singh.

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Season 1 - Episode 23 -- A Taste of Armageddon

The crew of the Enterprise visits a planet whose people fight a strange, computerized war with a neighboring enemy planet.

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Season 1 - Episode 24 -- This Side of Paradise

The Enterprise visits a planet where the inhabitants are kept in check by strange plant life.

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Season 1 - Episode 25 -- The Devil in the Dark

Captain Kirk faces off with a deadly subterranean creature that is killing off miners.

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Season 1 - Episode 26 -- Errand of Mercy

In a state of war with the Klingons, Kirk and Spock attempt to sway the primitive and incomprehensibly placid population of a planet to their side.

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Season 1 - Episode 27 -- The Alternative Factor

The crew of the Enterprise encounters a madman with the ability to jump from our matter universe to our opposite anti-matter universe.

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Season 1 - Episode 28 -- The City on the Edge of Forever

The crew of the Enterprise discover a portal through space and time, which leads to McCoy accidentally altering Earth history in the early 20th Century. Kirk and Spock follow him to help stop the Nazis from winning World War II.

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Season 1 - Episode 29 -- Operation: Annihilate!

The crew of the Enterprise encounter neurologically parasitic creatures that have destroyed a Federation colony, and are set to continue their murderous swarm across the galaxy.

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Episode summaries from Wikipedia.

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