As the U.S.S. Enterprise returns to spacedock for repairs following the battle with Khan in 2285. Kirk continues to mourn Spock's death. McCoy suddenly enters the Vulcan's sealed quarters, babbling incoherently. Upon reaching Earth, McCoy is hospitalized. Scotty is reassigned to the U.S.S. Excelsior and the newly formed Genesis Planet is decreed off-limits by Starfleet Command. Kirk is then informed that the U.S.S. Enterprise is to be decommissioned.
In Kirk's quarters, Sarek, Spock's father, confronts the Admiral, saying that Spock's body should have been returned to Vulcan so that his katra could have been stored in an ancient Vulcan repository on Mount Seleya. Sarek tells Kirk that he must retrieve the coffin from the Genesis planet and, since Spock performed a last-minute Vulcan mind-meld with McCoy, thus transferring his "katra" or spirit, the doctor must also return to Vulcan.
However, Starfleet refuses to allow the antiquated U.S.S. Enterprise to leave spacedock. Released from the hospital and faced with this news, McCoy tries to hire a craft to go back to the Genesis planet. He then starts a brawl and is subsequently arrested, pending further psychiatric examination. The arrest proves futile, though, when McCoy escapes with the help of Kirk, Scott, Sulu, Uhura and Chekov. The crew then beams aboard the deserted U.S.S. Enterprise. To avoid pursuit, Scotty removes an integral engine part from the U.S.S. Excelsior and, knowing that they've all probably destroyed their careers, the six friends take the Enterprise out for one final voyage.
Meanwhile, the Klingons have learned of the new Genesis Device and planet, and fear that it could be a new Federation weapon. Lead by the treacherous Captain Kruge, the Klingons set out to either destroy or capture the valuable device.
On board the U.S.S. Grissom, David Marcus and Lt. Saavik arrive at the Genesis Planet for scientific observation. They quickly discover a lifeform reading coming from the surface. Intrigued, the two beam to the planet's surface to find Spock's empty coffin. Tracing the lifeform reading, the two then find the living body of a child-Spock, aging with erratic rapidity but lacking a consciousness or spirit.
Suddenly, the Klingons arrive, destroying the Grissom and taking Saavik, Marcus, and the young Spock prisoner. Shortly thereafter, the U.S.S. Enterprise arrives in the Mutara Sector and is crippled by Kruge and his Klingon cohorts. With the Klingons threatening the lives of their prisoners, Kirk tries a bluff to regain control of the situation, but is unsuccessful. David Marcus is killed by the Klingon landing party. Faced with no other choice, Kirk surrenders the Enterprise to the Klingons, yet in a last-ditch effort to gain the upper hand, activates the starship's self-destruct mechanism. The small U.S.S. Enterprise crew then beams to the surface of the Genesis Planet, watching as their historic starship is destroyed in a streak of light, taking with it most of Kruge's nefarious crew.
Kirk and party rescue Spock and Saavik from the Klingons and learn that an unstable element used in the Genesis Device threatens the stability of the planet, which is likely to explode within minutes. One factor of this instability, however, is the rejuvenating effect it had on Spock's body. With the planet reaching critical mass, Spock finally achieves the age he was just before his death on the U.S.S. Enterprise. Kruge, still alive on the Klingon Bird-of-Prey and angry at the death of his comrades, beams down to the planet. There, he fights one-on-one with Kirk, eventually falling to his death. The Enterprise crew, Saavik, and Spock then escape in the Bird-of-Prey, just as the planet violently explodes, a victim of its own dangerous growth.
Under Sarek's diplomatic protection, the Klingon ship then speeds to Vulcan. Once there, the risky ceremony fal-tor-pan is performed, fusing Spock's katra, which resides in McCoy's mind, with the Vulcan's body. With the ceremony seemingly successful, a revived Spock begins the long journey of remembering his past and his friends. He questions why the Enterprise crew risked their lives and careers to rescue him. As his friend Jim reminds him, sometimes the "needs of the one outweigh the needs of the many."