Captain Kirk and his crew must deal with Mr. Spock's long-lost half-brother who hijacks the Enterprise for an obsessive search for God at the center of the galaxy.
When the newly-christened starship Enterprise's shakedown cruise goes poorly, Captain Kirk and crew put her into Spacedock for repairs. But an urgent mission interrupts their Earth-bound shore leave. A renegade Vulcan named Sybok has taken three ambassadors hostage on Nimbus III, the Planet of Galactic Peace. This event also attracts the attention of a Klingon captain who wants to make a name for himself and sets out to pursue the Enterprise. Sybok's ragtag army captures the Enterprise and takes her on a journey to the center of the galaxy in search of the Supreme Being.
It is the 23rd Century and vacationing Captain Kirk faces two challenges: climbing Yosemite's El Capitan and teaching campfire songs to Spock. But vacations are cut short when a renegade Vulcan with a startling secret hijacks the Enterprise in order to find a mythical planet. Kirk and his crew set out to stop this madman in an adventure that takes them to the center of the universe and, perhaps, before the face of God. With the crew under Vulcan control, the captain must rely on an unlikely alliance to save the galaxy. Meanwhile, a Klingon captain wants to make a name for himself and sets out to pursue the Enterprise and intercept Kirk.
- On a desert planet, Nimbus III (the Planet of Galactic Peace), a humanoid man has dug empty holes on the surface. While he digs another, he sees a dark horse and rider approaching. Panicked, he loads a crude rifle with ordinary stones and takes aim. The rider stops close by and approaches the man, informing him that he harbors a secret pain and that he needs to expose it. After a few moments of staring at the rider's serene face, the alien man is overcome with grief and says he feels like a great relief has overcome him. In return for this soul cleansing, the rider, who reveals himself as a Vulcan, asks the man to accompany him on an epic journey. To get there, they will need a starship.
Meanwhile, on Earth, Captain Kirk, Dr. McCoy and Spock are taking their shore leave in Yosemite National Park. Fretting, McCoy observes Kirk scaling El Capitan, muttering about Kirk's urge to play games with life. While he makes his ascent, Kirk is suddenly startled by Spock, who hovers nearby wearing jet-powered boots. Spock doesn't seem to understand Kirk's need to climb the mountain (Kirk says "Because it's there!"), citing the fact that Kirk will never break any records for free-climbing the mountain. Breaking records doesn't concern Kirk and he suggests that Spock find McCoy and pester him. Suddenly, Kirk loses his grip and falls; Spock races after him, catching his friend before impact. On Nimbus III, the Vulcan and his new followers survey the planet's one settlement, Paradise City. The move in and seize the city, capturing three delegates; General Korrd (a Klingon), Caithlin Dar (a Romulan), and St. John Talbot, (an Earthman). The Vulcan uses his persuasive power on all three, convincing them to join his cause. A distress signal is sent, something the Vulcan wants.
Kirk, Spock and McCoy later sit around a campfire and McCoy serves up homemade beans, laced with bourbon from his home region, Kentucky. The three discuss about Kirk's near-death experience; Kirk says he wasn't afraid because his friends were nearby. When pressed a little further, he says "I've always known I'll die alone." They sing "Row, Row, Row Your Boat" together, after educating Spock on the song's meaning - which has no meaning and is merely intended to be fun for a group to sing together. Their vacation is interrupted when Uhura shows up in one of the USS Enterprise's shuttlecraft and informs them that Kirk has been asked to deal with a sudden crisis in space. (Kirk had deliberately left his communicator behind so they wouldn't be disturbed.) Uhura also retrieves Sulu and Chekov from the forest after they lose their way on a hike.
On the Enterprise, things are chaotic. The ship's systems are constantly malfunctioning and Scotty, though happy to be working, still has his hands full bringing the ship to normal function. Transporters are also malfunctioning, hence the use of the shuttlecraft. On the bridge, Kirk receives his mission orders from Admiral Bennett; Kirk and his crew are to travel to Nimbus III and rescue the prisoners in Paradise City. A video showing the Vulcan's small army, the Army of Galactic Light, and their leader's demands is displayed for everyone. Seeing the Vulcan in the video, Spock is suddenly overcome. He explains to Kirk that the leader is Sybok, a Vulcan renegade who believed that the true meaning of Vulcan culture and existence was the embracing of emotion in contravention to Vulcan culture. Spock knew Sybok in his younger days, before he left Vulcan to follow his own pursuits.
In a remote sector of outer space, a Klingon Bird-of-Prey decloaks near an ancient Earth Gemini satellite. The ship's commander, Captain Klaa, fires blasters on it, destroying it. Clearly bored, Klaa desires a live target to engage. His first officer, Vixis, receives news of the distress call about the incident on Nimbus III. Klaa becomes excited, knowing that Kirk would be a formidable opponent. He orders his crew to set course for Nimbus III to pursue and intercept Kirk.
The Enterprise arrives on Nimbus III and sends a ground team down in a shuttle. On the surface, they first subdue an outpost outside Paradise City that is occupied by some of Sybok's followers - Uhura is the bait, doing an erotic fan dance to attract them. Donning the guards' clothing and using their mounts, they gain entry to Paradise City. At the same time, Chekov, who has been given the conn on the Enterprise, negotiates with Sybok from space as a distraction. Outside, Spock locates the prisoners, however, their ruse doesn't last and they are identified as infiltrators. A battle breaks out; several of Sybok's troops are stunned and Kirk makes his way into the tavern where the prisoners are being held. When Kirk finds them, they take him prisoner and lead him outside, where the rest of Kirk's team have also been captured.
Spock meets Sybok and informs his fellow Vulcan that he is under arrest. Sybok laughs, saying that he is happy to see Spock has developed a sense of humor. Spock deadpans that he was not kidding. Sybok turns his attention to Kirk and informs him he intends to steal the Enterprise, refusing to say what he needs it for. With no choice left to him, they all head back to the shuttle and take off. On the Enterprise, the Klingon Bird-of-Prey is detected right before it cloaks. Chekov orders the shields raised, which prevents the shuttle from docking. The usual procedure of using the tractor beam to lock on the shuttle will take far too much time, a period in which Klaa could easily cripple or destroy both vessels. Kirk orders Sulu to fly the shuttle in manually, an extremely dangerous procedure. Klaa's attack fails, and the shuttle crash lands in the docking bay. The Enterprise races off at warp speed, leaving Klaa excited that his target is so elusive.
In the cargo bay, Kirk and Sybok regain consciousness first and grapple over a crude rifle, Sybok seizing it first. He leads Kirk out at gunpoint; Kirk attacks him but fails to subdue the stronger Vulcan. The rifle is retrieved by Spock who points it at Sybok; despite Kirk's shouted order to shoot Sybok, he doesn't and they are imprisoned once again, much to Kirk's consternation. They are led away and Sybok requests a private moment with Sulu and Uhura.
In the brig, which is escape-proof, according to Spock (who acted as the test subject), Kirk admonishes Spock for not protecting his ship and his crewmates by shooting Sybok. Spock says that he could not shoot the Vulcan renegade because they are half-brothers, Sybok being the child of a relationship his father had with a Vulcan priestess before he met Spock's human mother. While they are trapped in the brig, Sybok reveals his plan; the Enterprise will travel through the galaxy's Great Barrier where he believes they will find a place called Sha-Ka-Ree, what humans would call Eden, or paradise. Kirk remarks that no one has ever returned from beyond the Great Barrier, nor has any probe. Spock remarks that Sybok has spent his entire life searching for the Vulcan paradise. Just then, they receive a message through the wall in ancient Morse Code ordering them to stand back. Scotty breaks through the wall, freeing them. They make their way through the ship's back tunnels; Scotty directs them to a turboshaft where they can reach the ship's observation deck to send a distress message to Starfleet. Scotty continues walking and bangs his head, falling unconscious. He is later found by Sulu and a small search party and taken to sick bay.
Meanwhile, Kirk, Spock and McCoy must climb the turboshaft's ladder by hand. They begin, but Spock disappears for a moment. Kirk and McCoy climb but are winded and exhausted after climbing a few decks. Spock floats to them using his jet-powered boots, however, they cannot take the weight of all three. They float down where Sulu and Sybok's men wait to recapture them. Spock activates the boot thrusters, a dangerous move, but one that propels them away from their captors. The three make it to the observation deck and send their message, however they are quickly found by Sybok himself. Sybok doesn't mind that the message was sent, saying that once his discovery is confirmed, everyone in the galaxy will want to come to the Barrier to see for themselves. Kirk still objects, demanding control of his ship. Sybok asks to be alone with Kirk, Spock and McCoy. He demonstrates the power he possesses to turn them into his followers. McCoy is forced to confront the death of his father from a disease that was cured a few months later. McCoy says he wanted his father to die with dignity rather than suffer and says that he feels as though a weight has been lifted from his heart. Spock is forced to confront his father's lifelong disapproval of his half-human ethnicity. Kirk refuses to succumb to Sybok's will, saying he needs his pain because it makes him human. Just then a signal from the bridge informs them that they have reached the Great Barrier.
Kirk allows the Enterprise to breach the Great Barrier. Inside, they find a barren planet bearing no life readings. Kirk, Spock, McCoy and Sybok take a shuttle down to the planet's surface. After walking a short distance, Sybok cries out, demanding to see God. Suddenly, several finger-like rocks burst from the surface, forming a semi-circle. Inside, a strange, glowing being that resembles the Christian image of God appears and greets them. Sybok informs it that he breached the Great Barrier to find it. The being informs Sybok that it wants to use the starship they came in to spread its benevolence to the rest of the galaxy. While the others stare in awe, Kirk asks the being why, if it is all-powerful, it needs a starship to travel from its home. When the being asks who Kirk is and why he would doubt him, Kirk suggests it should know already if it's actually God. Angered, the being suddenly shoots Kirk with an energy bolt, wounding but not killing him. Spock steps forward and demands an answer to Kirk's question and is also hit by the energy bolt. McCoy says he doubts any god that inflicts pain and Sybok asks the being who it really is; it takes the form of Sybok himself and Sybok realizes that the being is the sum total of his own obsession and arrogance. He tries to grab the being and help it release its pain and is consumed. As they escape from the being's lair, Kirk has Spock and McCoy beamed up. On the Enterprise, Spock sees that Klaa has arrived in his ship and his threatening the Enterprise with destruction. Spock turns to General Korrd to do something.
Kirk runs, finally being cornered by the evil being, when Klaa's Bird-of-Prey appears and blasts the creature into oblivion. Kirk thinks he's done for when he's beamed aboard the Bird-of-Prey. On board is General Korrd who barks a few orders to Captain Klaa. Klaa apologizes, saying he made an unauthorized attack on the Enterprise. He also introduces his new gunner, Spock, who fired the blast that destroyed the evil being on the planet below. Kirk says he thought he was finished, Spock informs him that he was never alone. Both Klingons and humans and other Federation races alike later attend a reception on the Enterprise that suggests a new era of cooperation has begun. The film closes with Kirk, Spock and McCoy back on Earth in Yosemite National Park once again sitting around a campfire and singing "Row, Row, Row Your Boat". Spock remarks "Life is but a dream."