is proceeding out from Starbase 12 investigating a distress signal, and finds a derelict spaceship from Earth’s late 20th century. Picking up very faint life signs, they intercept and determine there are approximately 70 humans in suspended animation aboard it. The ship’s hull is damaged by meteors but Spock determines that its name is the S.S. Botany Bay
, but there are no records. The ship appears to have left Earth in the 1990s, during the time of the Eugenics Wars. Kirk takes over a party to investigate, and has Lieutenant Marla McGivers accompany them as the ship’s historian. Beaming aboard, they discover that the passengers are in sleeper cells and one of the chambers begins to revive. McGivers is awestruck by the handsome figure of a man inside, which she identifies as the leader, set to awaken first. The chamber malfunctions and Kirk breaks it open, and McCoy tries to keep the leader alive. The man revives long enough to determine how long it’s been since they departed Earth, then passes out. McCoy beams back to the Enterprise
with him to try and keep him alive.
Further examination of the sleeper ship reveals most of the people have survived the centuries but they can find no records or documentation. Spock can’t find any computer records from the era either. McCoy manages to stabilize his patient, but notes that he is possessed of superior strength and endurance. Kirk meets briefly with McGivers and notes that she reacted less than professionally aboard the sleeper ship.
The leader revives in Sickbay and uses an antique scalpel to take McCoy hostage and get answers. McCoy is less than impressed and the man releases him and demands to meet with Kirk. The captain arrives but the leader gives nothing but his name: Khan. He refuses to answer any questions, particularly after Kirk refuses to awaken the other sleepers without more information. Khan does ask to review the ship’s technical manuals and update himself on the advances that have occurred in over two centuries, and Kirk agrees.
On the bridge, Spock reveals that Khan is almost certainly the result of superior breeding and that in 1993, a group of genetically manipulated “supermen” seized power for several years. The group’s size corresponds to the number of canister aboard the sleeper ship.
In Sickbay, the man revives on his own and takes McCoy hostage, then demands answers. McCoy refuses to back down and the leader releases him but demands to meet with Kirk. The man is evasive and gives nothing but his name: Khan. Kirk tells him they’re en route to Starbase 12 and refuses to activate the other canisters. Khan begs off pleading fatigue and asks permission to read the ship’s technical manuals. Kirk agrees and goes back to the bridge. There he and Spock theorize that Khan is the result of selective breeding, and that in 1993 a group of young supermen seized power in 40 nations simultaneously before turning on each other. Their numbers match the number of survivors on the sleeper ship.
McGivers goes to see Khan, supposedly with historical questions. However, she’s still awestruck with him and he takes advantage, seducing her and asking her to come back later. At her suggestion, they have a formal dinner party for Khan, and McCoy warns Kirk that she might be overwhelmed by Khan’s magnetism.
Khan goes to McGivers’ quarters and comments on her interest in great conquerors out of history. She’s been working on a painting of him and he says he’s flattered. She takes him to the dinner where Kirk and Spock take turns trying to find out more about him. They manage to bait him into a discussion about what his intent was in 1993: conquest. Khan pleads fatigue and leaves, and McGivers goes to apologize to him. Khan overpowers her and demands that she beg to stay with him, and she acquiesces. He then announces his plan to take over the Enterprise
and demands she give her loyalty to him. Once he agrees not to hurt anyone, she agrees.
Spock has managed to identify Khan as Khan Noonien Singh, leader of the supermen and ruler of most of Asia for three years, before they ended up fighting among themselves. Kirk confines Khan to his quarters and confronts him with their newfound knowledge. Khan doesn’t bother to hide his identity any further and expresses his contempt for Kirk and mankind in general. After the captain leaves, Khan uses his greater strength to force open the cabin door and knock out the guard, while McGivers takes over the transporter room. Khan beams over to the sleeper ship, revives the rest of his people, and sets the derelict adrift.
Kirk gets word too late that Khan has escaped and sealed off the bridge, trapping the command crew. Khan cuts off the air and demands their surrender, and when Kirk refuses he and the others pass out. Everyone else is taken to the briefing room where Khan demands their loyalty. When they refuse, he reveals that Kirk has been put in a decompression chamber and will be slowly killed. They still refuse, and a squeamish McGivers asks to go. Khan agrees and they lose the signal to the decompression chamber. Assuming Kirk is dead, Khan orders one of his men to take Spock there.
McGivers goes to the decompression chamber, knocks out the guard, and frees the captain. He knocks out Spock’s escort, and the first officer pumps anesthesia gas into the ship while Kirk goes after Khan. Khan manages to escape the gas, escape to Engineering, and cut off the ventilation to that section. Kirk arrives and Khan easily disarms him then reveals he’s set the ship’s engines on overload. With time running out, Kirk fights Khan and is initially overwhelmed by the genetically modified superman’s enhanced strength. Kirk manages to grab a tool and knock out Khan and stop the overload just in time.
Later, Kirk calls a hearing and drops the charges against Khan. Instead, he will dump Khan and his people on the uninhabited but inhabitable Ceti Alpha 5, and leave them to carve out whatever civilization they can. In love with Khan, and to avoid court martial, McGivers chooses to go with Khan. As they depart, Kirk wonders what they might eventually create.
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