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.
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.
After being tortured by the Klingons for information on the Guardian of Forever, an amnesia-stricken Kirk finds himself stranded in a 1950s mental institution. Meanwhile in the wake of the captain's disappearance and the crew's assumptions that he is dead, Spock is promoted to captain of the Enterprise which puts him at odds with the rest of the crew.