under the cut, a list of the episodes and their summaries, nabbed from wikipedia. this is not a signup post. this is just for reference.
---season one---
"The Cage"
The crew of the Enterprise follow a distress signal to the planet Talos IV, where Captain Pike is taken captive by a group of telepathic aliens. The events of this episode are revisited in the Season 1 episodes "The Menagerie, Parts I and II".
"The Man Trap"
The Enterprise visits planet M-113 for a routine medical inspection of archaeologists Robert and Nancy Crater, but find that Nancy Crater has been replaced by a deadly, shape-shifting creature.
"Charlie X"
While traveling about the Enterprise, a dangerous young man named Charlie Evans terrorizes the crew with his unusual mental powers.
"Where No Man Has Gone Before"
After the Enterprise attempts to cross the Great Barrier at the edge of the galaxy, crew members Gary Mitchell and Elizabeth Dehner develop "godlike" psychic powers which threaten the safety of the crew.
"The Naked Time"
A strange, intoxicating infection which lowers the crew's emotional inhibitions spreads throughout the Enterprise. A crew member's inebriated actions place the ship in danger, forcing Scotty to perform a hazardous and untested engineering procedure to save the ship from destruction.
"The Enemy Within"
While beaming up from planet Alpha 177, a transporter accident splits Captain Kirk into two beings: one "good," who acts weak and indecisive; and one "evil", who acts overly aggressive and domineering. Scotty must quickly repair the transporter system to reunite the two Kirks, and to rescue the landing party trapped on the surface of the icy planet below.
"Mudd's Women"
The Enterprise encounters interstellar con man Harry Mudd, who is arrested on outstanding charges while ferrying three extraordinarily beautiful women to a remote planet, destined to be wives for the miners located there. In actuality, the plain-looking women use illegal Venus drugs, which make them appear to be much more attractive than their natural appearance; after the drugs wear off, revealing Mudd's deception.
"What Are Little Girls Made Of?"
In search of Nurse Chapel's fiancé, renowned exobiologist Roger Korby, the Enterprise visits the icy planet Exo III, where Korby has discovered an ancient machine which allows him to duplicate any living person with an android replacement. Korby plans to use the machine to spread controlled androids throughout the Federation, and replaces Captain Kirk with such a duplicate in an effort to take over the Enterprise.
"Miri"
After discovering what appears to be a duplicate of the planet Earth, Captain Kirk and his landing party find a population ravaged by a strange disease, which has two effects: children are granted extraordinarily long life, but anyone who reaches puberty (including the adult landing party) develop painful sores which eventually kill the infected. The oldest child, a girl named Miri, develops a jealous affection for Captain Kirk, and works with the other children to kidnap Janice Rand after Kirk attempts to comfort the frightened yeoman.
"Dagger of the Mind"
At Tantalus V, a rehabilitation colony for the criminally insane, the inmates have taken over the asylum using a neural neutralizer, which is used to remove (or implant) memories from a subject's mind. One colony administrator, Simon van Gelder, escapes to the Enterprise, leading Captain Kirk to investigate the colony. While on the surface, Kirk is brainwashed and taken prisoner, but is helped by Dr. Helen Noel, a colleague from the Enterprise who joined him on the planet. Spock performs a mind-meld with van Gelder to counteract the effects of the neutralizer, healing his mind and allowing van Gelder to take over the colony after Kirk and Noel's rescue.
"The Corbomite Maneuver"
The Enterprise find an odd, glowing cube floating in interstellar space, which must be destroyed after it begins to emit dangerous radiation. Following the cube's destruction, an immense, glowing sphere called Fesarius races to the Enterprise's location, controlled by Balok, an alien who announces that he will destroy the Enterprise in retribution. Captain Kirk manages to bluff Balok into believing the Enterprise contains a deadly substance called Corbomite, which would severely damage any attacking ship. After managing to escape the Fesarius's tractor beam, disabling the alien ship, Kirk and a landing party board the sphere, discovering the true identity of the vessel's controller.
"The Menagerie, Part I"
After claiming to receive a subspace message, Spock diverts the Enterprise to Starbase 11 in order to visit the ship's previous captain, Christopher Pike, who has been severely injured and was using a wheelchair. Spock continues his deception by secretly transporting Pike to the Enterprise and uses falsified orders to take the ship to the quarantined world Talos IV (leaving Captain Kirk behind). Kirk and Commodore Mendez of Starbase 11 trail and eventually catch up to the Enterprise in a shuttle, where Spock surrenders. Mendez orders Spock to trial, where Spock uses the events of "The Cage" as his defense.
"The Menagerie, Part II"
Spock continues detailing the events of "The Cage" to the tribunal, using video evidence transmitted from Talos IV directly to the Enterprise. After witnessing the Talosians' capabilities of mental illusion, Kirk realizes that Spock intends to return Pike to the planet, where he can resume a normal life. Starfleet officially sanctions Spock's plan, and Pike is transported to the surface where his injuries appear completely healed.
"The Conscience of the King"
The Enterprise visits Planet Q at the request of Dr. Thomas Leighton, a friend of Captain Kirk. Leighton suspects that the leader of a famous acting troupe, Anton Karidian, is actually Kodos "The Executioner," the murderous former governor of planet Tarsus IV, where Kirk grew up. Kirk initially disagrees, believing the official story detailing Kodos' death years earlier, but begins to doubt after Leighton is found dead. To confirm Karidian's identity, Kirk arranges for the troupe to perform aboard the Enterprise.
"Balance of Terror"
While investigating a series of destroyed outposts, the Enterprise discovers a lone Romulan vessel with cloaking device. The Romulans, having never been seen by humans, are revealed to visually resemble Vulcans, which causes navigator Lt. Stiles to suspect Spock of treason. The two ships become locked in a cat-and-mouse battle through space, leaving the Enterprise seemingly crippled by Romulan weapons.
"Shore Leave"
Captain Kirk orders shore leave for the Enterprise crew on a seemily unihabited planet in the Omicron Delta system. The landing parties begin to see strange sights, such as the White Rabbit, Don Juan, and a sword-wielding samurai. Kirk sees (and fights) an image of Finnegan, a rival from his Starfleet Academy days. Spock discovers that the planet seems to be drawing a large amount of energy from the ship's engines, placing the Enterprise in danger.
"The Galileo Seven"
Spock and a scientific party are sent to study the Murasaki 312 quasar aboard the shuttle Galileo. During the survey, the Galileo is forced to make an emergency landing on the planet Taurus II, where the crew fight the planet's dangerous inhabitants. As the crew begin to make repairs, Scotty determines that the shuttle does not have enough fuel to reach orbit carrying all seven passengers, and Spock must contemplate leaving some of his fellow crew behind.
"The Squire of Gothos"
The Enterprise discovers a rogue planet drifting through space, inhabited by an eccentric being named Trelane who uses his apparently unlimited power over matter and form to manipulate the crew.
"Arena"
The Enterprise comes under attack by unknown aliens while investigating the near-destruction of the Cestus III colony. While chasing the aliens into unexplored space, both ships are captured by the powerful Metrons, who force Kirk and the alien captain (later identified as a member of the Gorn race) to trial by combat: the winner's vessel will be set free, while the loser's ship will be destroyed.
"Tomorrow Is Yesterday"
After accidentally traveling back in time to 1969, the Enterprise rescues USAF Captain John Christopher from his crippled fighter jet. The crew struggles to return to their own time, while simultaneously returning Christopher to the Air Force, removing his knowledge of the future, and all record of contact with the Enterprise.
"Court Martial"
Captain Kirk is placed on trial for negligence after Lt. Commander Ben Finney is killed during a severe ion storm. Kirk maintains that his actions were proper and should not have lead to the officer's death, but the Enterprise computer records disagree, showing Kirk ejecting Finney's research pod before placing the ship at red alert status.
"The Return of the Archons"
The Enterprise discovers a planetary population controlled by a powerful being called Landru. While investigating, Captain Kirk and his landing party are taken captive and discover that the Enterprise crew will be the next to be "absorbed" into Landru's control.
"Space Seed"
The Enterprise discovers an ancient sleeper ship, the SS Botany Bay, which escaped from Earth's Eugenics Wars in the late twentieth century. The genetically engineered passengers, led by war criminal Khan Noonien Singh, seize control of the Enterprise and attempt to destroy the ship. (This episode serves as the backstory to the second Star Trek film).
"A Taste of Armageddon"
On Eminiar VII, the Enterprise finds a civilization at war with its planetary neighbor. Unable to discern any signs of battle from orbit, Captain Kirk leads a landing party to the surface where he discovers the entire war is fought by computer. Even though the war is simulated, citizens who are listed as virtual casualties still report to termination booths to be killed for real. After the Enterprise is destroyed in an attack simulation, Kirk must fight to keep his crew from death.
"This Side of Paradise"
Despite exposure to deadly radiation, the Federation colony on Omicron Ceti III appears to be thriving. A landing party from the Enterprise investigates, finding the colony's population to be healthy beyond explanation. Leila Kalomi, an old friend of Mr. Spock, shows the landing party strange flowers that seem to impose a state of pure bliss on all exposed to its spores (even Spock). The spores effects spread rapidly throughout the Enterprise, causing the crew to mutiny against Captain Kirk.
"The Devil in the Dark"
Dispatched to the mining colony on Janus VI, the Enterprise is tasked to investigate rumors of a strange, subterranean creature responsible for destruction of equipment and the deaths of fifty miners. Kirk and Spock discover a silicon-based life form, a Horta, which lives in the surrounding rock. After wounding the creature, Spock performs a mind meld, discovering the reason behind the Horta's attacks.
"Errand of Mercy"
Peace negotiations have collapesed between the Federation and the warlike Klingon Empire. The Enterprise is ordered to protect Organia, a peaceful planet located near the Klingon border. Kirk and Spock beam to the surface to warn the Organians about the Klingons, but soon a Klingon fleet arrives, forcing the Enterprise to abandon the duo on the planet. The natives protect Kirk and Spock, even as Kor, the new Klingon governor, orders mass executions of the Organian people. As both Federation and Klingon fleets converge above the planet, Kirk and Spock execute a daring raid on the Klingon headquarters in an effort to destabilize their control over the planet.
"The Alternative Factor"
While orbiting an apparently dead planet, the Enterprise seems to experience a strange moment of "nonexistance." Captain Kirk discovers a man named Lazarus on the planet below, who claims the effect was caused by his "enemy," later revealed to be an insane version of Lazarus from an alternate dimension. The sane version of Lazarus asks for Kirk's help in defeating his counterpart.
"The City on the Edge of Forever"
After accidentally overdosing on a powerful stimulant, Dr. McCoy acts erratically and disappears through the Guardian of Forever, a newly-discovered time portal on a remote planet. Kirk and Spock follow after learning that McCoy somehow changed history. Arriving in the 1930s, the duo meet Edith Keeler, a New York social worker who gives them a place to stay. As the days pass, and McCoy is nowhere to be seen, Kirk finds himself falling in love with Keeler... but Spock discovers that Keeler must die to restore the timeline.
"Operation: Annihilate!"
The Enterprise arrives at Deneva - the home of Captain Kirk's brother, Sam - and discovers that the entire planet has been infested with large, amoeba-like aliens that have attacked and killed much of the human population. One of these aliens attaches itself to Spock, who volunteers to become a subject in Dr. McCoy's medical tests. After McCoy accidentally blinds Spock during one of his test procedures, the doctor must quickly find a way to neutralize the dangerous creatures.
---season 2---
"Amok Time"
Mr. Spock shows evidence of starting to lose control over his emotions. When he insists that he needs to return home to Vulcan, despite being engaged in an important diplomatic mission, Kirk forces him to admit that Vulcan biology requires him to take a mate. After diverting to Vulcan against Starfleet's direct orders, Kirk finds himself in a life-or-death struggle against Spock, at the instigation of Spock's wife-to-be.
"Who Mourns for Adonais?"
The crew of the Enterprise are held captive by an alien who claims to be the Greek god Apollo.
"The Changeling"
The crew of the Enterprise deals with Nomad-an indestructible, planet-destroying space probe that thinks Kirk is its creator. Star Trek: The Motion Picture was in part an expansion of this episode.
"Mirror, Mirror"
A transporter mishap slips Captain Kirk and his companions into a parallel universe, where the Enterprise serves a barbaric Empire instead of the Federation. This episode spun off several plotlines in Deep Space Nine and Enterprise.
"The Apple"
The crew of the Enterprise visits a mysterious paradise planet which they discover is controlled by a computer.
"The Doomsday Machine"
The Enterprise plays a deadly game of cat-and-mouse with an alien planet-killing machine.
"Catspaw"
Two powerful aliens threaten the well-being of the Enterprise and her crew with their magical powers.
"I, Mudd"
Captain Kirk and the crew has a second run in with the con man, Harry Mudd, this time finding him as the king of a planet of androids.
"Metamorphosis"
A shuttle crew from the Enterprise encounters a castaway (who appears to be Zefram Cochrane, the inventor of warp drive) and his mysterious alien companion.
"Journey to Babel"
While the Enterprise is transporting dignitaries to an important peace conference, an assassin is discovered.
"Friday's Child"
The crew of the Enterprise become entangled in a planet's tribal power struggle.
"The Deadly Years"
Strange radiation exposes the command crew of the Enterprise to the effects of rapid aging.
"Obsession"
Captain Kirk becomes obsessed with destroying a murderous entity that killed many of the crew of his old ship.
"Wolf in the Fold"
Mr. Scott is implicated in a series of bizarre murders.
"The Trouble With Tribbles"
Tribbles, purring, limbless, and fertile disrupt the exploitation of a disputed planet between the Klingons and Federation.
"The Gamesters of Triskelion"
Captain Kirk and his companions are sent to fight as gladiators for the gambling entertainment of three disembodied beings.
"A Piece of the Action"
The Enterprise visits a planet with an Earth-like, violent, 1920s gangster culture.
"The Immunity Syndrome"
The crew of the Enterprise encounters an energy-draining space creature.
"A Private Little War"
Captain Kirk must decide how to save a primitive people from the technological interference of the Klingons.
"Return to Tomorrow"
Telepathic aliens take control of Kirk and Spock's bodies with the intention to build new, mechanized bodies for themselves.
"Patterns of Force"
The crew of the Enterprise visits a planet dominated by a Nazi culture and at war with its planetary neighbor.
"By Any Other Name"
Beings from the Andromeda Galaxy steal the Enterprise, technically modify it, and attempt to return home.
"The Omega Glory"
Captain Kirk must battle a deadly virus and prevent a meaningless intertribal war.
"The Ultimate Computer"
A new computer system causes havoc while being tested aboard the Enterprise.
"Bread and Circuses"
Captain Kirk and his companions are forced to fight in gladiatorial games on a planet modeled after the Roman Empire.
"Assignment: Earth"
During a historical research mission in 1968, the Enterprise encounters an intergalactic traveler named Gary Seven.
---season three---
"Spock's Brain"
Captain Kirk pursues aliens who have stolen Spock's brain.
"The Enterprise Incident"
The crew of the Enterprise attempts to steal a Romulan cloaking device.
"The Paradise Syndrome"
A mysterious alien device on a planet with a predominantly American Indian culture erases Captain Kirk's memory, and he begins a life with them as a member of their tribe.
"And the Children Shall Lead"
The crew of the Enterprise rescues a group of children stranded on a planet, along with their evil "imaginary" friend.
"Is There in Truth No Beauty?"
The Enterprise travels with an alien ambassador who must travel inside a special black case because his appearance causes insanity.
"Spectre of the Gun"
For having trespassed on an alien world, Captain Kirk and his companions are forced to re-enact the famous shoot-out at the O.K. Corral.
"Day of the Dove"
An alien energy-based life form that feeds on negative emotions (such as fear, anger, hatred) drives the crew of the Enterprise into brutal conflict with the Klingons.
"For the World is Hollow and I Have Touched the Sky"
The crew of the Enterprise rush to stop an asteroid from colliding with a Federation world, but discovers that the inside of the asteroid is inhabited.
"The Tholian Web"
Captain Kirk is caught between dimensions while the Enterprise is trapped by an energy draining web spun by mysterious aliens.
"Plato's Stepchildren"
The crew of the Enterprise encounters an ageless and mischievous race of psychic humanoids who claim to have organized their society around Ancient Greek ideals.
"Wink of an Eye"
Invisible "time-accelerated" aliens take over the Enterprise and attempt to abduct the crew for use as "genetic stock".
"The Empath"
While visiting a doomed planet, the landing party is subject to torturous experiments to test an empathic race.
"Elaan of Troyius"
Captain Kirk hosts a spoiled princess, who must bring peace to a star system at war.
"Whom Gods Destroy"
Captain Kirk visits a mental health facility and confronts an insane starship captain who believes he is destined to control the universe.
"Let That Be Your Last Battlefield"
The Enterprise picks up the last two survivors of a war-torn planet who are still committed to destroying each other aboard the ship.
"The Mark of Gideon"
A race of overpopulated aliens abduct Kirk to solve their problem.
"That Which Survives"
The crew of the Enterprise visits an abandoned outpost guarded by a mysterious computer.
"The Lights of Zetar"
Strange, energy-based alien life forms threaten the Memory Alpha station and the Enterprise crew.
"Requiem for Methuselah"
The crew of the Enterprise encounters an immortal human who lives as a recluse on his own planet.
"The Way to Eden"
The Enterprise is hijacked by a criminal doctor and his loyal, hippie-like followers who are attempting to find paradise.
"The Cloud Minders"
Kirk races against time to acquire plague-fighting minerals from a world in the midst of a civil uprising.
"The Savage Curtain"
Aliens force Kirk and Spock to battle illusionary villains in a test of good versus evil.
"All Our Yesterdays"
Kirk, Spock, and McCoy are trapped in the past on a world threatened by a supernova.
"Turnabout Intruder"
Kirk's consciousness becomes trapped in the body of a woman bent on killing him and taking over his command while inhabiting his body.