The crew of the starship USS Enterprise is enjoying shore leave at Yosemite National Park when they are called back to duty to respond to a crisis on the planet Nimbus III, the so-called "Planet of Galactic Peace." Upon arrival, they discover that a renegade Vulcan named Sybok has taken the planet's inhabitants, including representatives of the Federation, Klingon, and Romulan governments, hostage. Sybok seeks the starship's assistance to embark on a quest to find the mythical planet Sha Ka Ree, which he believes is the original home of life and possibly God. Displaying the ability to alleviate emotional pain, Sybok convinces many of the Enterprise's crew to join his cause, creating discord and challenging Captain James T. Kirk's command.

While dealing with the internal strife caused by Sybok's influence, Kirk and his closest officers, Spock and Dr. McCoy, are challenged by their own personal demons and relationships with one another. As they make the perilous journey to the center of the galaxy, where Sha Ka Ree is rumored to exist, they must also contend with a persistent Klingon warship, determined to exploit the situation for the glory of the Klingon Empire. Complicating their mission, they begin to realize that Sybok's vision may be driven by more than mere conviction, as they face the vast unknown and the potential dangers that lie at the heart of the Milky Way.