Admiral Kirk and his bridge crew risk their careers stealing the decommissioned Enterprise to return to the restricted Genesis Planet to recover Spock's body.
In the wake of Spock's ultimate deed of sacrifice, Admiral Kirk and the Enterprise crew return to Earth for some essential repairs to their ship. When they arrive at Spacedock, they are shocked to discover that the Enterprise is to be decommissioned. Even worse, Dr. McCoy begins acting strangely and Scotty has been reassigned to another ship. Kirk is forced to steal back the Enterprise and head across space to the Genesis Planet to save Spock and bring him to Vulcan. Unknown to them, the Klingons are planning to steal the secrets of the Genesis Device for their own deadly purpose.
Admiral Kirk's defeat of Khan Noonien Singh and the creation of the Genesis Planet are empty victories. Mr. Spock is dead and Dr. McCoy is, seemingly inexplicably, being driven insane. Then an unexpected visit from Spock's father provides a startling revelation: McCoy is harboring Spock's living essence. With one friend alive and one not, but both in pain, Kirk attempts to help his friends by stealing the Enterprise and defying Starfleet's Genesis quarantine. However, the Klingons have also learned of the Genesis Device and race to meet Kirk in a deadly rendezvous.
- Having survived her battle with Khan Noonien Singh, the USS Enterprise is returning to Earth. With a few hours left in their journey, Admiral Kirk remarks in his log that there is a heavy feeling amongst the crew on the ship, having lost their science officer, Captain Spock, whom sacrificed himself to insure the Enterprise would not be destroyed by Khan. Kirk has Uhura check for a hailing signal from Starfleet but finds there isn't one. When asked by a cadet if they will receive a hero's welcome at home, Kirk thinks they will since they have paid with their dearest blood.
In a remote area of space, a Klingon female, Valkris, waits on a small Earth freighter for a signal from her commanding officer. Commander Kruge responds and Valkris transmits stolen data to him on Project Genesis. When asked by Kruge if she had seen the information, she replies she had. Kruge informs her that it's unfortunate that she had. With the captain of the freighter asking when he will be paid, Kruge's ship, a Klingon Bird-of-Prey, deactivates its cloaking device and swings into attack, blasting apart the freighter and flying off.
On Earth, the Enterprise arrives at the orbiting Spacedock. While the ship docks, the crew catches sight of Starfleet's newest and most advanced ship, the USS Excelsior. Sulu remarks that the Excelsior has a new technology called transwarp drive. Mr. Scott is skeptical but scornful, however Kirk scolds him gently, saying "Young minds, fresh ideas." A warning alarm suddenly sounds; someone has broken into Mr. Spock's quarters which Kirk had ordered sealed. Kirk goes there himself and finds Dr. McCoy, whom appears to be suffering from mental trauma. He informs Kirk that he left him back on Genesis and that he has to climb the steps of Mount Selaya on the planet Vulcan. McCoy collapses, unconscious, and Kirk calls for the medics.
However, the crew of the Enterprise is not given a ceremonial reception from Starfleet. They are received by Admiral Morrow who has nothing but bad news for them: Kirk will not be allowed to return to the Genesis Planet to retrieve Spock's body. Project Genesis has become a galactic controversy and only the science teams will be allowed access to the planet. The crew are sworn to secrecy regarding the forbidden subject. Scotty will be reassigned to the Excelsior to help with engineering development on the new ship. Worst of all, the Enterprise is to be decommissioned from service.
Back on Kruge's ship, he and his first officer study the Genesis Device and determines that it can be an invincible weapon. Her orders the crew to set course for the Genesis Planet. On board one of Starfleet's science vessels, the USS Grissom, Dr. David Marcus and Lt. Saavik approach the Genesis Planet. They scan the surface of the planet and find varying environmental conditions. They also locate the photon tube in which Spock's body was sent to the planet's surface during his funeral services. They ask permission to beam down to the planet, a request that Captain Esteban is reluctant to allow. He eventually gives them permission.
Back on Earth, at Kirk's apartment, he and his comrades share a drink honoring Spock. They also discuss McCoy's condition, who is noticeably absent and allegedly sedated in a medical facility. Kirk answers a ring at his door and is surprised to see Spock's father, the Vulcan ambassador, Sarek. Kirk asks his friends to leave and speaks privately with Sarek, who is quite upset with Kirk for leaving Spock behind. Sarek speaks of Spock's Vulcan katra, his soul, that can possibly be returned to his body. Saying that Spock would not have spoken openly about his final wishes, he asks Kirk to allow a mind-meld with him. Sarek recounts Kirk's and Spock's final moments together but does not find a trace of Spock's katra. As he starts to leave, Kirk stops Sarek and informs him that even in a situation as desperate as the near-destruction of the Enterprise and Spock's efforts to prevent it, Spock would have transferred his katra to someone else. Kirk reviews the ship's recording of Spock's last conversation with Dr. McCoy and sees that Spock had mind-melded with him after rendering him unconscious before entering the warp drive chamber. Sarek informs Kirk that he must bring both McCoy and Spock to Mount Selaya on Vulcan where a ritual can be performed to restore Spock's mind to his body. Kirk says it will be difficult, but he will attempt the rescue.
Back on Genesis, David and Saavik find Spock's photon tube, and his burial robe inside. The photon tube is also covered with a strange species of slimy, orange slugs. David deduces that they are the evolutionary descendants of microbes present on the photon tube before it was sent to the planet. They also notice that the weather conditions on the planet change very rapidly. They hear a child's cry coming from a nearby cave and find a Vulcan child: Spock. They dress him again in his robe and contact the Grissom about the discovery. However, Esteban has to interrupt communication with them when Kruge's Bird-of-Prey enters the sector and attacks. Kruge's gunner fires a photon torpedo at the Grissom, destroying her. Angered over being denied Federation hostages, Kruge shoots his gunner with a blaster, disintegrating him. His officer, Torg, informs him that there are members of the Grissom's crew on the Genesis Planet below and that he will still have a chance to take prisoners. Kruge beams down with two of his crew and they search for Saavik and David. They reach the photon tube and find huge, lamprey-like creatures, the next evolution of the small creatures David and Saavik found earlier. They pick up David and Saavik's signal on a scanner and head toward them.
On Earth, Kirk asks Admiral Morrow to allow him to return to the Genesis Planet to rescue Spock. Morrow refuses, citing that Genesis is off limits and a forbidden subject. He also expresses doubt about what he calls Vulcan mysticism. Kirk behaves as though he sees Morrow's point and agrees not to attempt a voyage to Genesis. Outside the bar where he met Morrow, he finds his friends and informs them that despite Morrow's refusal, they will go ahead with their plans. In another bar, Dr. McCoy meets with an alien pilot to arrange his own charter to Genesis. The alien, who has a booming voice, speaks loudly enough to get McCoy noticed by Federation officers that have followed him. They arrest him and put him in the brig. After making his arrangements for travel, Kirk visits McCoy in his cell and informs him about Spock's mind-meld. McCoy is given a tranquilizer and Sulu, using martial arts, subdues the guards. In a transporter room on Spacedock, Uhura is present when Kirk, Sulu and McCoy arrive. She blackmails the officer she works with in the facility and beams her three friends aboard the Enterprise. On board already is Scotty, who has reworked the ship's control systems to be operated from the bridge. Kirk gravely informs his crew that the should not join him on his mission so as to avoid prosecution. They refuse to leave.
As they prepare the ship for departure, they are hailed by Federation security to return the Enterprise, a warning that Kirk orders ignored. The ship moves out, heading directly for the dock's space doors, which remain sealed. Following several attempts, Scotty is successful in opening them, allowing the Enterprise to escape. Meanwhile, on board the Excelsior, Captain Styles receives orders to pursue and stop Kirk. The Enterprise goes to warp speed and streaks away. The Excelsior powers up, Styles planning to use the ship's experimental transwarp drive to overtake the Enterprise. When he orders the transwarp drive activated, it fails, leaving the Excelsior stranded outside Spacedock. On board the Enterprise, Scotty gives a handful of circuits to McCoy, admitting he had sabotaged the other ship.
On Genesis, Saavik confronts David about the unstable nature of the planet. David admits that he used a volatile substance, protomatter, in the Genesis matrix. Protomatter may have advanced David's research, but has created a planet that is aging too rapidly to be habitable. The same effect is also advancing Spock's development and David and Saavik conclude that they must escape the planet before it destroys itself and to stop Spock's rapid aging. Spock is also experiencing a biological process called pon farr, where transitional periods occur every seven years in which a Vulcan male develops into an adult. Saavik is able to soothe the painful process for Spock.
The three are later captured by Kruge and his crew. Kruge informs them of his intention to seize the Genesis Device, despite David's insistence that it doesn't work. Of course, Kruge intends to use it as a weapon. The renegade commander is called back to his ship when the Enterprise arrives on Genesis. Kruge orders the cloaking device engaged and they wait for the Enterprise to close the distance for attack. On board the Enterprise, Chekov loses a signal on his sensor as the Bird-of-Prey cloaks. The crew looks closely at the viewscreen and Kirk notices a shimmering distortion. As Kruge orders his ship decloaked and prepares to fire, Sulu identifies it and Kirk orders the firing of photon torpedoes. The Bird-of-Prey is hit directly and begins to tumble, but quickly recovers, having suffered minimal damage. Kirk orders the Enterprise's shields to be raised, but Scotty reports that the ship's systems are malfunctioning due to the unexpected battle, and before the crew can do anything else the Klingons fire a photon torpedo at the ship's warp engines, causing devastating damage which destroys the Enterprise's propulsion and weapons systems, leaving the ship a lifeless hulk.
Kirk hails the Klingon warship and demands to know why they are there and why they attacked. Kruge realizes that he has the advantage, since Kirk would have just destroyed the Bird-of-Prey if the Enterprise was capable, and demands that Kirk surrender, saying that the very possession of the Genesis Device by the Federation brands war criminals. He also reveals that he is holding Saavik, David and Spock prisoner. He allows communication with them and Saavik informs Kirk that Spock is with them. David informs Kirk that the planet will destroy itself and that Spock must be taken off immediately. To show his intentions are sincere, Kruge orders one of his prisoners executed. One of the Klingons draws a dagger and prepares to kill Saavik, David intervenes and fights with the Klingon, who stabs David to death. Kirk is overwhelmed by the brutal death of his son. After a few moments, he invites Kruge to send over some of his crew to retrieve them and the Genesis materials. He orders McCoy and Sulu to the transporter room, leaving himself, Scotty and Chekov on the bridge. The three activate the Enterprise's self-destruct sequence and leave for the transporters. They beam down to the planet just as Kruge's troops arrive. They find the bridge and discover the countdown; Kruge's order to beam them back comes too late and the Enterprise explodes. On the planet, Kirk and his friends watch as the Enterprise falls out of orbit and burns up in the Genesis atmosphere. Kirk asks "My God, Bones, what have I done?" McCoy replies "What you always do: turn death into a fighting chance to live."
Kirk and his team find Saavik and Spock just as Spock, in a rage of pain, throws one of his Klingon captors, possibly killing him. Kirk kills the second guard. Saavik informs Kirk that the Genesis effect will kill Spock if they don't leave the planet immediately. Just then Kruge beams down and holds them all at gunpoint. He orders his crew to beam up everyone but Kirk and Spock. Kruge demands Genesis; Kirk says he will give it to him if he beams Spock up, which Kruge refuses. The two fight, hand-to-hand while the ground shifts and rumbles with earthquakes around them. They battle to the edge of a cliff, part of which falls away under Kruge's feet, leaving him dangling over a chasm of molten rock. Kirk offers to pull the Klingon up; when he does, Kruge tries to pull down Kirk with him. Kirk kicks Kruge several times in the face, finally dislodging him; Kruge falls hundreds of feet and burns up in the extreme heat below. Kirk runs back to Spock, grabs Kruge's communicator and calls for beam-up, imitating the Klingon's voice. He and Spock arrive safely on the Bird-of-Prey, which has been commandeered by Kirk's comrades. They speed off as the Genesis Planet explodes.
The ship arrives on Vulcan where Sarek has made preparations at Mount Seleya. Spock's body is brought up to an altar on the mountain where the high priestess, T'Lar, awaits with Sarek. Sarek asks for the ancient ritual of fal-tor-pan, the refusion of Spock's katra with his body. T'Lar warns that the ritual has succeeded only in legend. She also warns McCoy that the ritual carries as much danger for him as it does Spock. McCoy agrees to participate. An indeterminate amount of time passes while T'Lar performs the ceremony. The Enterprise crew waits anxiously until McCoy walks down from the altar, apparently fine. Kirk asks Sarek if the ritual was successful, to which Sarek replies "Only time will tell." Clad in a white robe, Spock descends, at first oblivious to Kirk's and his old friends' presence, however he stops and recognizes Kirk. He asks "Ship out of danger?" to which Kirk says that he saved them all. A note of recognition in his face, Spock says "Jim. Your name is Jim." Kirk and his friends are overjoyed.