Time in the galaxy has stopped running in its normal course. That can mean only one thing—the Guardian of Forever is malfunctioning. To save the universe, Starfleet Command reunites three of its most legendary figures—Admiral James T. Kirk, Spock of Vulcan, and Dr. Leonard McCoy—and sends them on a desperate mission to contact the Guardian, a journey that ultimately takes them 5,000 years into the past. They must find Spock's son Zar once again, and bring him back to their time to telepathically communicate with the Guardian.

But Zar is enmeshed in troubles of his own, and soon Kirk, Spock, and McCoy find themselves in a desperate struggle to save both his and their world.