第 3 季 共 24 集
播出时间：1968年9月21日
第 1 集 Spock's Brain
播出时间：1968年9月21日
An alien female beams aboard the ship and, after incapacitating the rest of the crew, surgically removes Spock's brain. Kirk and the crew have just hours to locate and replace it before Spock's body dies.
第 2 集 The Enterprise Incident
播出时间：1968年9月28日
The crew of the Enterprise are on a secret mission to steal a Romulan cloaking device.
第 3 集 The Paradise Syndrome
播出时间：1968年10月5日
An alien device on a primitive planet erases Captain Kirk's memory, and he begins a new life with the planet's indigenous people.
第 4 集 And the Children Shall Lead
播出时间：1968年10月12日
On a distant planet, Kirk, Spock and McCoy find a scientific team dead, and their children who, unknown to the crew, have great powers at their disposal.
第 5 集 Is There in Truth No Beauty?
播出时间：1968年10月19日
The Enterprise travels with an alien ambassador whose appearance induces madness.
第 6 集 Spectre of the Gun
播出时间：1968年10月26日
Having been found trespassers into Melkotian space, Captain Kirk and his companions are sent to die in a re-enactment of the gunfight at the O.K. Corral.
第 7 集 Day of the Dove
播出时间：1968年11月2日
An alien force drives the crew of the Enterprise into brutal conflict with the Klingons.
第 8 集 For the World Is Hollow and I Have Touched the Sky
播出时间：1968年11月9日
The crew of the Enterprise rush to stop an asteroid from colliding with a Federation world, but discover the asteroid is actually an inhabited generation ship.
第 9 集 The Tholian Web
播出时间：1968年11月16日
Captain Kirk is caught between dimensions while the crew of the Enterprise works to retrieve him. All the while, the Tholians demand that the Enterprise leave their space.
第 10 集 Plato's Stepchildren
播出时间：1968年11月23日
The crew of the Enterprise encounters an ageless and sadistic race of humanoids with the power of telekinesis and who claim to have organized their society around Ancient Greek ideals.
第 11 集 Wink of an Eye
播出时间：1968年11月30日
Invisible "time-accelerated" aliens take over the Enterprise and attempt to abduct the crew for use as "genetic stock".
第 12 集 The Empath
播出时间：1968年12月7日
While visiting a doomed planet, the landing party is subject to torturous experiments by powerful aliens.
第 13 集 Elaan of Troyius
播出时间：1968年12月21日
The USS Enterprise ferries a spoiled princess whose betrothal to a royal Troyian is hoped will bring peace to a star system at war.
第 14 集 Whom Gods Destroy
播出时间：1969年1月4日
Captain Kirk faces off with a demented shape-shifting starship captain determined to control the universe.
第 15 集 Let That Be Your Last Battlefield
播出时间：1969年1月11日
The Enterprise encounters two duo-chromatic and mutually belligerent aliens who put the ship in the middle of their old conflict
第 16 集 The Mark of Gideon
播出时间：1969年1月18日
A race of overpopulated aliens abduct Captain Kirk to solve their problem.
第 17 集 That Which Survives
播出时间：1969年1月25日
Kirk, McCoy, and Sulu are stranded on a barren planet where a mysterious woman attempts to kill them one at a time, while the Enterprise must travel halfway across the galaxy to rescue them.
第 18 集 The Lights of Zetar
播出时间：1969年2月1日
Strange incorporeal aliens threaten the Memory Alpha station and the Enterprise.
第 19 集 Requiem for Methuselah
播出时间：1969年2月15日
The crew of the Enterprise encounter an immortal human in this science fiction variation on Shakespeare's The Tempest.
第 20 集 The Way to Eden
播出时间：1969年2月22日
The Enterprise picks up a group of space ""hippies"" looking for Eden.
第 21 集 The Cloud Minders
播出时间：1969年3月1日
Captain Kirk races against time to acquire plague-fighting minerals from a world in the midst of a civil uprising against a grievous social class disparity.
第 22 集 The Savage Curtain
播出时间：1969年3月8日
Aliens force Captain Kirk and First Officer Spock to join forces with "Abraham Lincoln" and "Surak" to battle villains in a contest of good vs. evil.
第 23 集 All Our Yesterdays
播出时间：1969年3月15日
Kirk, Spock and McCoy are trapped in two parts of another planet's past—a world threatened with destruction when its sun goes supernova.
第 24 集 Turnabout Intruder
播出时间：1969年6月4日
The Enterprise is in danger when Janice Lester, one of Kirk's former lovers, steals his body.
