On a barren planet called Nimbus III, a strange, messianic figure wanders through the wilderness, freeing poor colonists from their "secret pain," whatever that means. Nimbus III was originally meant to symbolize the peace between the Klingon Empire, Romulan Empire, and Earth-led Federation of Planets, as proven by the presence of three ambassadors in the capital, Paradise City. This peace is a sham, however.
On Earth, Captain James T. Kirk is mountain climbing in Yosemite with his buddy Leonard "Bones" McCoy, the medical officer on his ship, the USS Enterprise. Kirk falls but is saved at the last moment by Spock, his first mate. Spock is half-human and half-Vulcan, the latter species being known for its devotion to logic over emotion.
Meanwhile, on Nimbus III, the strange cult leader has amassed a huge following. The cult members overtake Paradise City, easily besting the armed guards and taking the ambassadors as hostages. But what's this guy's plan? Who knows. We didn't write this thing.
Our heroes learn of this unfolding disaster and are requested by Starfleet to check it out. Enterprise is currently in the middle of repairs, but they'll have to go regardless. Meanwhile, a Klingon captain named Klaa learns this same information and also heads to Nimbus III.
After seeing a video sent by the hostage-takers, Spock realizes that he knows the weirdo cult leader. According to him, the guy had been a friend of his on Vulcan, but he had been exiled because he advocated for emotion over logic.
Before they can delve deeper, our heroes arrive at Nimbus III. Kirk, McCoy, and Spock head down to the surface for a clandestine assault, while the rest of the crew stays aboard Enterprise to serve as a diversion. The assault goes well at first, but it falls off the rails when our heroes locate the hostages—and the hostages capture them. Huh?
The ambassadors are now loyal to the cult leader, Sybok. Sybok acts like he and Spock used to be really close. Suspicious…
While Sybok forces his hostages to fly him back to Enterprise, the Klingons arrive. Klaa learns that Captain Kirk is around and changes his plans—now the maximum way to attain glory is to kill Kirk. Boy, that's just what we need, more complications.
The shuttle manages to dock on Enterprise amid the Klingon assault. Spock grabs a gun but shockingly allows Sybok to take it without putting up a fight. Sybok casts his spell over the other crew members before sending Spock, Kirk, and McCoy to the brig.
There, Kirk and McCoy learn a shocking truth: Sybok is Spock's half-bro. Whoa. So that's why he couldn't shoot him. As they discuss a further plan of action, our heroes are freed by Scotty, the ship's engineer. While Scotty goes to repair the ship's transporter system, the trio heads up to an emergency communications room.
They send off a message, but it doesn't go to Starfleet—it's intercepted by Klaa. He's hot on their trail. Meanwhile, Sybok reveals over the ship's intercom that he plans to go to the center of the galaxy, where he will find Sha Ka Ree, the mythical place from which creation sprang. Oh, yeah—and God will be there, too.
Sybok nabs our heroes. Drat. He performs a weird therapy session with McCoy by unearthing painful memories about McCoy's father's death, which seems to put the doc under his spell. He does the same with Spock, but far less successfully. Before he can move on to Kirk, however, the ship reaches the Great Barrier, which surrounds Sha Ka Ree.
Despite its intimidating nature, the Great Barrier is nothing to write home about. When our heroes pass through it, they see a lone planet. It must be Sha Ka Ree.
Could that whack job be right?
Kirk, Spock, McCoy, and Sybok head down to the planet's surface. They meet a being that identifies itself as God who asks them to use Enterprise to carry his knowledge throughout the galaxy. Kirk is skeptical; God responds by blasting him in the chest with energy. Ditto with McCoy and Spock when they voice their concerns.
The entity reveals that it is, in fact, a prisoner on this planet. It manipulated Sybok into coming here so the dude would break him out of jail. Furious at this deception, Sybok sacrifices himself to take down the baddie, but he utterly fails. He does buy enough time for Spock and McCoy to be beamed up to Enterprise, however.
Spock and McCoy reach the ship just as the Klingons arrive. Great. In a deft move, Spock uses the Klingon ambassador from Nimbus III to convince the Klingons to defend Kirk instead of killing him. Who knows how he manages that, but the result is that the Klingons blow up the impostor deity just as it's about to kill Kirk. Phew.
So, what else is there to do but party? The film ends with a big celebration featuring the crew of Enterprise, Klaa's Klingon warriors, the cultists from Nimbus III, and the three ambassadors. Why weren't we invited? Regardless, this represents the real peace that has just been forged between these formerly warring factions.