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.

Although he has been missing for several years and the entire town thinks her father has abandoned her family, Meg steadfastly believes the best and protects her younger brother, Charles Wallace, from the brunt of the rumors and taunting. It is he, however, who convinces her to join him, the school sports star Calvin, and three unusual women on an interplanetary voyage to rescue their father from a vast evil.

Dispatched on a rescue mission to the farthest reaches of space, the USS Enterprise is ambushed by Krall, a ruthless enemy sworn against the Federation. Crash-landing on an uncharted hostile world, Captain Kirk, Spock, and the crew are separated with no means of escape. Only Jaylah, a rebellious alien warrior, can help them reunite and find a way off the planet in a race against time to stop Krall's deadly army from triggering all-out galactic war....