| Episode | Description |
|---|---|
| Beyond the Farthest Star | The Enterprise is dragged off course by Questar M-17, an imploded negative star mass, and meets a strange shapeless being. |
| Yesteryear | By using the Guardian of Forever, Kirk, Spock, and the historian Erikson explore the planet Orion's past. When they return, there is no record of Spock. |
| One of Our Planets is Missing | The Enterprise crew learns that a massive, planet-destroying extragalactic entity has entered Federation space and threatens every planet in the galaxy. | The Lorelei Signal | The Enterprise enters an uncharted sector of space where Federation and Klingon vessels have been reported missing every 27 years. |
| More Tribbles, More Troubles | The tribbles return for more trouble as the Enterprise encounters Cyrano Jones, the Klingons and a new breed of the popular pest. |
| The Survivor | A long-lost philanthropist, Carter Winston, is discovered on board a damaged one-man vessel and is reunited with his fiancée on board the Enterprise. |
| The Infinite Vulcan | While visiting a new planet, Sulu is poisoned and Spock becomes cloned by the Phylosians, a plant-like species. |
| The Magicks of Megas-Tu | While investigating the theory of creation, the Enterprise is caught inside an energy/matter tornado and pulled to the center of the galaxy. |
| Once Upon a Planet | The Enterprise returns to the amusement planet where the crew had once taken shore leave, but this time things go wrong. |
| Mudd's Passion | The Enterprise is ordered to find Harry Mudd, a Federation outlaw, who is accused of selling a fake love potion to miners. |
| The Terratin Incident | A strange flash of light paralyzes the entire Enterprise crew and all organic matter begins to shrink. |
| The Time Trap | While exploring the Delta Triangle, where many starships have disappeared, the Enterprise is attacked by several Klingon vessels. |
| The Ambergris Element | The Enterprise arrives to study the planet Argo, a water-based planet where earthquakes caused the land masses to sink. |
| The Slaver Weapon | When a rare artifact of the Slaver culture, a time-stopping stasis box, is being delivered to Starbase 25, it registers that another one is nearby. |
| The Eye of the Beholder | The disappearance of a scientific team lures the Enterprise to investigate near Lactra VII. |
| The Jihad | On Vedala, Kirk and Spock are summoned to learn about a stolen religious artifact that could ignite a galaxy-wide holy war, a jihad. |
| The Pirates of Orion | A dreaded disease, choriocytosis, strikes the Enterprise. All except Spock are cured, as the illness is fatal only to Vulcans. |
| Bem | Starfleet, eager to open diplomatic relations with the medically advanced Pandronians, assigns Enterprise to host one of their representatives. |
| The Practical Joker | While studying an asteroid, the Enterprise is attacked by three Romulan vessels which claim that the Federation ship has trespassed into Romulan space |
| Albatross | The Enterprise arrives at Dramia I to deliver medical supplies when Dr. McCoy is arrested for mass slaughter and imprisoned. |
| How Sharper Than a Serpent's Tooth | While tracking a probe, the Enterprise encounters an alien vessel that is surrounded by an energy field which proceeds to encompass the Federation ship. |
| The Counter-Clock Incident | A hyper-accelerated alien ship drags the Enterprise into a nova and both arrive in an antimatter universe where time flows backwards. |