• James T. Kirk: William Shatner
• Spock: Leonard Nimoy
• Leonard "Bones" McCoy: Deforest Kelley
• Chekov: Walter Koenig
• Sulu: George Takei
• Uhura: Nichelle Nichols
• Sybok: Laurence Luckinbill
• Klingon Ambassador:Charles Cooper
• Terran Ambassador:David Warner

On the planet Nimbus III, a central location where one ambassador each from the Federation, Klingon Empire and Romulan Empire have met to discuss solutions to the mutual hostility each government holds for the others, talks have virtually ceased despite the arrival of a new Romulan ambassador and Nimbus III has become an arid desert. A renegade Vulcan - apparently breaking from the tradition of his race and embracing emotions and impulses - has generated a strong following on the planet and takes the three ambassadors hostage. The Vulcan, Sybok, then sends a message to the delegates' governments, demanding a fair hearing of his demands in exchange for the hostages' lives. A Klingon vessel, commanded by trigger-happy Captain Klaa, heads for Nimbus III with Klaa spoiling for a fight with the legendary Enterprise. The Enterprise arrives first, and Kirk mounts a rescue operation involving distracting the guards, but he finds himself being held at gun point by the hostages he was meant to rescue, Kirk realizes that the affair has been a trap. Sybok now intends to hijack the Enterprise, and succeeds in earning the loyalty of Sulu, Uhura and Chekov by "releasing" them from painful memories in their lives. Sybok sets the Enterprise on a course to the Great Barrier at the center of the galaxy, where he believes he will find the mythical planet Sha Ka Ree and, according to Sybok's theory, that world's inhabitant - God.

Surviving the supposedly deadly trip through the barrier, the Enterprise arrives at an uncharted planet, convincing many of the ship's crew that Sybok may be right. In their excitement, no one notices that Klaa's ship is now arriving at Sha Ka Ree as well. Kirk, Spock, McCoy and Sybok fly a shuttle to the surface and, although initially finding no sign of life, encounter the projection of an enormous face which claims to be God and greets Sybok. However, when the being insists that the enterprise be brought in close enough that he may meld with it for the journey beyond the Great Barrier, Kirk is suspicious and questions the being's authenticity.

The creature lashes out at Kirk and Spock when they doubt his identity, and Sybok realizes that it is not God. Grappling with the entity so that the others may escape, Sybok gives Kirk time to order a torpedo fired at the creature, but it is not easily killed. When they return to the shuttle, Kirk, Spock and McCoy discover that it has been crippled by the creature, and Kirk orders Scotty to beam Spock and McCoy up. As soon as they have safely returned to the Enterprise, Klaa opens fire on the Enterprise, damaging the transporters once more. Spock convinces General Koord, the Klingon delegate from Nimbus III and one of Sybok's recent converts, to use his rank to commandeer Klaa's ship and rescue Kirk. Koord agrees, and Spock takes over the gunner's seat on the Klingon ship to destroy the God impostor in time to save Kirk. The Klingons and the Enterprise leave Sha Ka Ree peacefully (and after profuse apologies from Klaa), offering some hope for a peaceful future, in which the formerly disgruntled Nimbus III delegates promise to take a more active interest.

Although the movie's end seemed to touch on a Federation peace with the Klingons, the situation obviously was a small instance of cooperation between the two, as "Star Trek VI : The Undiscovered Country" indicated that they were still deadly enemies.