After receiving a distress call, the USS Enterprise, commanded by Captain James T. Kirk , is assigned to investigate an intruder attacking the Primus IV colony. Once there, the crew encounters a strange alien life form that can produce visions of personal events displaced in time. These visions may hold the key to better understanding the threat they are about to encounter.

The timestream was changed by sending a Doomsday Machine back in time. There, the Doomsday Machine destroyed several planets, manufactured more Doomsday Machines, and began what is now known as the Doomsday Wars. Captain Kirk, in command of the USS Farragut, is sent back in time to prevent this from happening and save the future.

A group of Klingons are planning to expand their territory, but while the crew is doing everything in their power to stop the invaders, one famous Lieutenant has to fight off his own demons when an old disease starts to age him at an alarming pace. Celebrating 40 years of Star Trek, Walter Koenig returns as Pavel Chekov, the best weapons officer the USS Enterprise will ever have.

During an emergency transport, Sulu returns 30 years older than when he left and with his daughter.

Ensign Peter Kirk asks his uncle James to marry him and his lover, Lt. Alex Freeman. But first both of them join a security team headed by Mr. Spock investigating a distress call by the U.S.S. Copernicus.

Spock, Peter Kirk & Alex Freeman are stuck aboard the U.S.S. Copernicus which is invested with Regulan Bloodworm and has to be destroyed. However, they meet two researchers aboard who claim to have a cure for the infestation.

The Enterprise encounters a mysterious alien entity which causes a crew member to give birth to a child with remarkable - and dangerous - powers.

The Enterprise must reach the Klingon home world to convince their emperor not to start a war.

A tortured and amnesiac Captain Kirk is dumped into Eath's past by the Klingons, where he ends up in a 1950's mental institution. Meanwhile, a shattered Enterprise crew tries to survive with its new captain: Mister Spock.

Captain Kirk and the Enterprise investigate the devastation of Lappa III, apparently by the terraforming efforts of Dr. Carol Marcus.