With the assistance of the Enterprise crew, Admiral Kirk must stop an old nemesis, Khan Noonien Singh, from using the life-generating Genesis Device as the ultimate weapon.
It is the 23rd century. Admiral James T. Kirk is an instructor at Starfleet Academy and feeling old; the prospect of attending his ship, the USS Enterprise--now a training ship--on a two-week cadet cruise does not make him feel any younger. But the training cruise becomes a deadly serious mission when his nemesis Khan Noonien Singh--infamous conqueror from late 20th century Earth--appears after years of exile. Khan later revealed that the planet Ceti Alpha VI exploded, and shifted the orbit of the fifth planet as a Mars-like haven. He begins capturing Project Genesis, a top secret device holding the power of creation itself, and schemes the utter destruction of Kirk.
It is the 23rd century. The Federation starship USS Enterprise is on routine training maneuvers, and Admiral James T. Kirk seems resigned to the fact that this may well be the last space mission of his career. But Khan Noonien Singh is back. Aided by his exiled band of genetic supermen, Khan--infamous conqueror from late 20th century Earth--has raided Space Station Regula One, stolen a top secret device called Project Genesis, wrested control of another Federation starship, and now schemes to set a most deadly trap for his old enemy Kirk... with the threat of a universal Armageddon!
- A female Vulcan officer sits in the command chair on the bridge of the USS Enterprise. While the senior crew and some cadets work at their consoles, the officer, Lt. Saavik (Kirstie Alley), makes a log entry, then orders Commander Sulu (George Takei) to project a course to avoid entering the Neutral Zone at the Klingon border.
Suddenly, Uhura (Nichelle Nichols) receives a distress call from the Kobayashi Maru, a ship that has struck a gravitic mine near Altair VI, inside the Neutral Zone. Despite warnings from both Sulu and Spock (Leonard Nimoy), Saavik orders the ship to enter the Neutral Zone in order to beam the survivors aboard. Upon entering the Neutral Zone, the Enterprise is confronted with three Klingon battle cruisers, which open fire. The Enterprise is heavily damaged; many of the bridge officers are killed. Saavik has no choice but to order the surviving crew to abandon ship.
However, the filtered voice of Admiral James T. Kirk (William Shatner) is suddenly heard. The bridge viewscreen slides aside, revealing a lighted room beyond. The Kobayashi Maru was a Starfleet Academy simulation, one Saavik does not believe to have been a fair test of her command abilities. Kirk explains that the no-win scenario is a situation every commander may face, and that how one faces death is equally important as how one faces life. Saavik seems ruffled at the advice, but Kirk offers that now she has something new to think about. As he leaves, Dr. McCoy asks Kirk why the Enterprise will not once again receive an experienced crew. Kirk replies that space exploration should be left to younger crews, a remark that puzzles Uhura.
Outside the simulator room, Spock awaits Kirk's opinion of the cadets' performance. Kirk notes that the trainees wreaked havoc with the simulator room and Spock alike. Spock recalls Kirk's own Kobayashi Maru, noting that Kirk himself took the test three times and that his final solution was unique. Kirk then thanks Spock for his birthday present, an antique copy of Charles Dickens' novel "A Tale of Two Cities". Spock then leaves to catch a shuttle to board the Enterprise and await Kirk's arrival--he will later inspect the ship. Kirk then retreats to his apartment, to be greeted by Dr. Leonard "Bones" McCoy (DeForest Kelley), who presents him with two gifts; a bottle of finely-aged Romulan ale and a pair of antique eyeglasses. Noticing Kirk is going through a mid-life crisis, he questions whether Kirk really wants to carry on the duties of an admiral, or to be galaxy hopping on a starship. McCoy urges Kirk to get back his starship command, and the two share a drink sitting by the fireplace.
Meanwhile, Commander Chekov (Walter Koenig) is on board the USS Reliant, which is orbiting the planet Ceti Alpha VI. The crew is searching for a lifeless planet to satisfy the requirements of a test site for the Project Genesis experiment, a terraforming program proposed to the Federation by a group of scientists. Although Ceti Alpha VI should be incapable of supporting life, Chekov detects a minor energy reading on a scanning device. After conferring with Carol Marcus (Bibi Besch), the head scientist of Project Genesis, who informs them there cannot be a single shred of life on the planet, Chekov and Terrell plan to investigate the life-reading themselves. Chekov and Captain Terrell (Paul Winfield) beam down to the surface. Upon arrival, they fight their way through a blinding sandstorm until they discover and enter what appears to be a crashed derelict vessel.
They soon discover that the derelict is actually cargo carriers assembled together from the SS Botany Bay, a ship Chekov remembers all too well. Panicked, he rushes a confused Terrell toward the exit, only to find that a group of strangely-dressed people are waiting outside. Chekov and Terrell are taken prisoner, and their captor reveals himself as Khan Noonien Singh (Ricardo Montalban). He identifies the rest of his group as the remaining survivors of his crew. Khan reveals that 15 years earlier, Captain Kirk exiled Khan and his followers to Ceti Alpha V after the genetically-engineered supermen nearly captured the Enterprise (a reference to the series episode "Space Seed"). Khan says that six months after they were marooned, Ceti Alpha VI exploded, destroying Ceti Alpha V's ecosystem and shifting its orbit and position in space. The crew of the Reliant thought they were orbiting Ceti Alpha VI, when in reality they were orbiting Ceti Alpha V instead.
Khan blames Kirk for the death of his wife (presumably Lt. Marla McGivers, an Enterprise crew member who joined Khan in exile) and plans to avenge her. In order to find out why the two are there, Khan forces juvenile Ceti eels (unpleasant-looking creatures) into their ears. Once inside their victims, Khan explains, the Ceti eels wrap themselves around the cerebral cortex of the brain, rendering the victim susceptible to any command and to interrogation. Khan explains further: As the Ceti eels grow and mature inside the brain, the victim is slowly driven insane, followed later by death. Khan calmly asks them about their mission and where he can find Kirk.
Using Chekov and Terrell as his servants, Khan and his henchmen seize control of the Reliant and escape from Ceti Alpha V. Khan later has Chekov contact Carol Marcus at their remote research station, Regula 1, and inform them that Ceti Alpha VI is ready for the testing of Genesis and that Starfleet has ordered all Genesis components to be taken there immediately when Reliant arrives in about three days. Carol is adamant, stating that no one will have access to Genesis without proper approval. Carol's own son, David Marcus, also a scientist and working with his mother's team on the project, asks Chekov who gave the order, Chekov says it came from Admiral Kirk. Furious at Starfleet, Carol meets with her team to figure out what to do.
Under the command of Captain Spock, the Enterprise is being assigned to train cadets from Starfleet Academy, and Kirk, McCoy, Sulu and Uhura come aboard to assist in a short training cruise. Admiral Kirk is inspecting the trainee crew, who are learning the ropes on the Enterprise. The Enterprise leaves her orbiting drydock, under the command of an officer trainee, Lieutenant Saavik, the first of her race to graduate at her level. Once clear, Spock gives Sulu navigational control and the Enterprise speeds away on the training cruise.
Kirk later receives a distress call from Regula 1. Kirk orders the call to be patched through to his quarters, a communication he is nervous about since he and Carol Marcus were romantically involved in the past, a relationship that went sour and resulted in the birth of their son, David.
Furious, Carol asks him why he is taking Project Genesis away from her. Confused, Kirk incredulously denies having any involvement with the order. The already weak transmission becomes even more garbled and communication is soon lost, having been jammed by a nearby Reliant. After consulting with Starfleet Command, Kirk assumes command and orders the Enterprise to set a course for Regula 1.
While en route, Kirk asks Spock and McCoy to join him in becoming familiar himself with Project Genesis. Hosted by Carol Marcus, a video summary explains that the project involves the sophisticated terraforming of dead planets, making them habitable. Because the video was produced a year before, Kirk assumes they have reached "Stage Two" of the project. McCoy asks what the result of using such a device on a living world would be and Spock concludes it would destroy any existing life. McCoy sees the project as a dangerous venture that could be turned into a deadly weapon and is angry at Spock's logical attitude about the dangers. Just at that moment, Saavik calls them over the intercom and informs them that they have made contact with the Reliant.
The Enterprise approaches the Reliant. Despite being unable to contact them, Kirk is not concerned at first and is reluctant to raise shields as, Saavik reminds him, rules and regulations prescribe. However, when the Reliant gives a false status report, Kirk orders a yellow alert, which proves be too little, too late. The Reliant raises its shields, powers up its weapons, and opens fire. The Enterprise is caught off-guard and is badly damaged. Having been on board the Enterprise once before, Khan knows exactly where its weak points are, disabling the Enterprise's main energizers and warp core, leaving only auxiliary power on the ship, and mortally injuring several cadets, including Midshipman 1st Class Peter Preston (Ike Eisenmann), Scotty's (James Doohan) nephew. Engines are down, shields inoperative, and there is only enough power for a few short phaser shots, which isn't enough against the Reliant's shields.
Khan hails Kirk, who is shocked to see Khan in command of the Reliant. Khan arrogantly announces his plans to destroy the Enterprise, to which Kirk pleads with Khan to take him as prisoner and spare his crew. Khan agrees, but also demands all information on the Genesis Device. Kirk pretends to comply, but he actually has Spock transmit a signal using the Reliant's prefix code that causes the Reliant to lower her shields. Despite his intelligence, Khan is still very inexperienced with the command of a starship. When he realizes what Kirk is doing, he is unable to immediately locate the controls to override the command lowering the shields. With the few shots auxiliary power can give him, Kirk is able to fire at the Reliant, damaging photon controls and the warp drive. Khan is reluctant to withdraw, but the rest of his crew remind him that the Enterprise, with its disabled power systems, cannot escape. Both ships limp away for repairs and the match ends in a stalemate. Sulu congratulates Kirk on his victory, however Kirk admits that he had misjudged the situation and encourages Saavik to quote Starfleet regulations whenever applicable.
Kirk surveys the wounded in sickbay and attends to Peter Preston on his deathbed. With impulse power restored, the Enterprise arrives at Regula 1. Kirk assembles a landing party, and Saavik reminds him of General Order 15 barring him from beaming into a dangerous situation without armed escort. They find the station abandoned and several of the station's scientists gruesomely murdered, and discover Chekov and Terrell, semi-conscious and abandoned inside a storage container. Still quite dazed, Terrell and Chekov relate their experiences with Khan and inform Kirk that Khan is quite insane. When asked where the crew of the Reliant are, Terrell says they were marooned by Khan on Ceti Alpha V. They find that the station's records of the Genesis Device have been erased by the Regula 1 staff. Exploring the station leads them to a transporter that has recently been activated. Checking the coordinates, Saavik realizes they beamed into the Regula planetoid nearby, assuming they had gone to where the second stage of the Genesis experiments were conducted, which would be underground. Kirk asks for a damage report from the Enterprise. Knowing that Khan is listening to their communications, Spock exaggerates and reports that "by the book", hours would seem like days and that transporters will be available in two days, hinting to Kirk that they can be beamed back in about two hours.
Using the transporter coordinates, they beam down to the asteroid and materialize inside a rocky chamber. The Genesis Device is there, but before Kirk can move, he is attacked by his and Carol's son, David Marcus (Merritt Butrick), who accuses Kirk of trying to steal Genesis. Carol tries to defuse the situation, but before she can elaborate, the team is threatened by Chekov and Terrell. Terrell and Chekov reveal they are still under Khan's control and Terrell is ordered by Khan to kill Kirk. However, Terrell resists Khan and the Ceti eel causes him extreme pain. To escape it, he turns his phaser on himself and commits suicide. Chekov collapses and the Ceti eel slurps out of his ear and is promptly vaporized by Kirk. The Genesis Device is suddenly beamed away. Kirk grabs Terrell's wrist communicator and taunts Khan, informing Khan that he will have to come down to the planetoid if he wishes to kill Kirk. Shocked to find Kirk alive and well, Khan vows to leave him marooned on Regula for eternity. An enraged Kirk screams at Khan, who cuts communication.
Kirk avoids Carol and David's questions about Khan by asking for food. Carol and David show Kirk, McCoy and Saavik the Genesis cave, which was created by a smaller Genesis Device: deep within Regula a stable ecosystem now exists, having been created in one day. Before Kirk and Carol join them, they both speak briefly about their past relationship and reach a moment of reconciliation.
In the cave, Saavik asks Kirk, who is casually eating an apple, about his performance on the Kobayashi Maru scenario. McCoy informs her that Kirk is the only Starfleet cadet to beat the no-win scenario. However, Kirk admits he reprogrammed the simulation, making it possible to save the ship and her crew. David chuckles and says he cheated, and Kirk qualifies that he changed the conditions of the test also citing that he had received praise for original thinking and that he does not believe in the no-win scenario. Kirk then promptly contacts the Enterprise and Spock says they should prepare for transport. Kirk smiles at a dumbfounded Saavik and asserts that he doesn't like to lose. Saavik questions what happened throughout the transport and Kirk reminds her of Starfleet Regulation 46A: Spock had modified his report (hours instead of days) to deceive Khan because their adversary may have been monitoring the Enterprise's transmissions. When Saavik suggests that Spock lied, Spock merely replies he "exaggerated."
Unfortunately, the Enterprise cannot defend herself fully against the Reliant. Spock suggests that the Enterprise set course for the nearby Mutara Nebula, where ionized gases will disrupt the sensors and shields of both vessels, essentially rendering them blind and evening the odds. Khan orders the Reliant to pursue, but his crew is reluctant, as they know the shielding and sensor systems will be rendered useless. Khan's second-in-command, Joachim, reduces speed, believing the situation to be too dangerous.
Back on the Enterprise, Spock notes that the Reliant is reducing speed and seems to be backing away from the pursuit. To ensure that Khan will follow him, Kirk has Uhura contact the Reliant and proceeds to taunt his nemesis, saying "We tried it once your way, Khan. Are you game for a rematch? Khan... I'm laughing at the superior intellect." Enraged by the mockery, Khan behaves irrationally and orders full impulse power and despite Joachim's protests, recklessly launches into the pursuit again. The Battle of the Mutara Nebula ensues. Both ships are quite hampered by the conditions whereas the Enterprise in open space would have been the more vulnerable vessel.
A game of cat-and-mouse follows. Computer targeting does not function, so both crews must rely on manual firing commands based on their view of the opposing ships on the visual display, which is mostly static. Being more experienced, Sulu is able to make better guesses and inflict slight damage but both vessels largely miss each other. As they maneuver half-blind around the nebula, suddenly the static on the Enterprise viewscreen clears enough to reveal that both ships are about to collide. They swerve apart and narrowly miss colliding, and at such point-blank range, even manual firing is sufficient for each vessel to inflict key hits on the other. The Reliant manages to destroy the port torpedo launcher of the Enterprise, which then returns fire and damages the Reliant's bridge, causing an explosion that kills several of the ship's bridge crew including Joachim, whom Khan vows to avenge. In the exchange, serious damage is inflicted again and Scotty is forced to shut down Enterprise's main reactor, which has flooded a control compartment with radiation.
Nevertheless, Kirk is able to ambush the Reliant because of his superior starship combat experience. When Spock suggests that Khan is inexperienced and is using a strategy based on two-dimensional thinking, Kirk orders the Enterprise to drop several thousand meters below the Reliant. The Reliant glides past above the Enterprise. A shaken, but physically recovered Chekov enters the bridge and offers his assistance. Kirk asks him to go to the weapons station. Khan isn't prepared for the Enterprise to descend before he passes overhead and then ascend directly behind him. The Reliant is hit with several phaser blasts, and a torpedo breaks off her port nacelle. The Reliant is crippled and drifts away, trailing plasma. Most of Khan's crew is killed in the process, and Khan himself is left crippled and barely alive by the explosions on the bridge.
In her final attempt to kill Kirk, the mortally wounded Khan activates the Genesis Device, knowing that the shock wave from it will destroy the Enterprise and her crew. The Enterprise cannot escape the large explosion that the device will trigger. Spock exits the bridge and decides to sacrifice his life by entering the radiation-filled engine room and repairing the broken warp drive, while Kirk orders a withdrawal at best possible speed. Realizing that the ship is doomed, Spock silently leaves his console.
On the Reliant's bridge, watching the Enterprise retreat and believing that the ship cannot escape the blast, Khan quotes from the novel "Moby Dick": "From hell's heart, I stab at thee. For hate's sake, I spit my last breath at thee." Khan finally collapses. Spock arrives in engineering, only to be stopped by Dr. McCoy from entering a lethally irradiated compartment that is part of the warp drive system. After initially appearing to comply with McCoy, an apologetic Spock nerve-pinches McCoy, and mind-melds with the doctor, saying simply "Remember..." He dons work gloves, enters the chamber, and begins to repair the main reactor, the radiation from the console spewing directly in his face. Moments later, McCoy regains consciousness and he and Scotty plead in vain with Spock to stop what he is doing.
Spock is successful and the warp engines come on line just in time, and the Enterprise streaks away just as the Genesis Device and Reliant explode. The Mutara Nebula condenses around the explosion, creating a newborn planet. Kirk contacts engineering to congratulate Scotty, but he is unconscious due to the radiation he had been exposed to. McCoy gravely replies that Kirk needs to come down; Kirk notices the empty chair at the science station. A look of dawning horror suddenly fills Kirk's face as he rushes down to Engineering to find Spock, dying. Kirk calls out for Spock and follows as the Vulcan staggers to the side of the transparent radiation barrier, finally resting against it.
Spock attempts with difficulty to explain to Kirk his reasoning: "Don't grieve, Admiral. It is logical. The needs of the many outweigh..." to which Kirk finishes, "the needs of the few," and Spock nods. "Or the one..." However, Spock states that he himself never took the Kobayashi Maru test until now, and asked Kirk, "What do you think of my solution?" Stricken with grief, Kirk cannot reply. Spock says "I have been and always shall be your friend. Live long and prosper." He holds out his hand, in the traditional Vulcan salute, and Kirk presses his hand up to the glass as well, watching as Spock slumps to the floor, and dies. It takes all of his resolve to keep his composure as he sees his closest friend die in front of him.
Spock's funeral is later held on the torpedo deck. Kirk says a few words in Spock's honor, concluding with a befitting statement: "Of all the souls I have encountered in my travels, his was the most... human." While Scotty plays "Amazing Grace" on the bagpipes, Spock's body is launched in a torpedo casing into the atmosphere of the newborn Genesis Planet. Later, trying to relax in his quarters, Kirk tries to read his copy of "A Tale of Two Cities". He sees that the glasses given to him by McCoy are broken and he tosses them aside. David visits him and they both reconcile, accepting that they are father and son. Kirk is humbled, especially when David mentions that Kirk had faced death before but never the death of a close and trusted friend like Spock.
On the bridge, the crew and Carol Marcus look at the newborn world formed by the Genesis Wave. McCoy expresses the feelings of Kirk by saying "He's not really dead as long as we find ways to remember him." The Enterprise sets its course for Earth, with a stop at Ceti Alpha V to pick up the Reliant crew. The shot dissolves to various scenes of the ecosystem of the Genesis Planet, finally arriving at Spock's photon tube. In voiceover, we hear Spock's voice reciting the opening Star Trek monologue.