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.