The Federation Starship U.S.S. Enterprise is on routine training maneuvers, and Admiral James T. Kirk seems resigned to the fact that this may be his last space mission. But Khan--a brilliant renegade of 20th Century Earth--is back with his exiled band of genetic supermen and setting a deadly trap for his old enemy Kirk ... with the threat of a universal Armageddon!

On the day of James Kirk's birth, his father dies on his ship in a last stand against a mysterious alien vessel. He was searching for Ambassador Spock, who is a child on Vulcan, disdained by his neighbors for his half-human nature. Twenty years later, Kirk has grown into a young troublemaker. He is inspired by Capt. Christopher Pike to fulfill his potential in Starfleet, even though he annoys his instructors. Suddenly, there is an emergency on Vulcan...

When the crew of the Enterprise is called back home, they find that an unstoppable force of terror from within their own organization has detonated the fleet and everything it stands for, leaving the world in a state of crisis. With a personal score to settle, Captain Kirk leads a manhunt to a war-zone world to capture a one-man weapon of mass destruction.

Branded as fugitives by the Federation they swore to protect, the crew dutifully returns to Earth to face charges for crimes committed in the course of rescuing a resurrected Spock, but while en route, they learn that Earth is being ravaged by a strange alien probe demanding a response from a life form that no longer exists.