Khan makes a statement in this episode that really doesn't ring true. Bemoaning the lack of progress in Humanity over the last two centuries he comments that if one improves a machine one might double productivity, but if one improved Man himself the one could gain a thousandfold. This is simply the exact opposite of the truth. Khan himself claims to have five times Kirk's strength. So if a job involved lifting heavy loads, he might increase productivity fivefold. Possibly more if he has enhanced endurance as well - but there's a limit to the improvements there, since there are after all only so many hours in a day.
Compare this to Kirk using a bulldozer. A really large dozer can lift more than a hundred tons in one scoop - and that's just present day technology, not whatever antimatter-powered anti-gravity tractor beam bulldozers they might have in a few hundred years. One man with a dozer could move more dirt in a day than fifty Khans could ever hope to. And so it goes with almost every arena; who would you bet on, Khan running or Kirk on a motorbike? Khan swimming or Kirk in a speedboat? Over and over, it's the genetic supermen that offer a marginal improvement and the machines that show the true way of the future.
Spock can find no record of the ship, though he notes that information from the period is fragmentary given that the Eugenics wars resulted in massive disruption at the time. The ship is named Botany Bay, a little ominous as it is named for a prison colony. Seventy two of the passengers remain alive, still in stasis. They decide to take the ship in tow and head for the nearby Starbase 12.
In sickbay the patient wakes and attempts to force McCoy to explain what is happening by threatening him with a scalpel. McCoy reacts cooly, impressing the man with his courage. He finds that the man is named Khan, and informs him of his situation. Kirk arrives to talk to him, filling in some details, but Khan seems reluctant to give any information in return, claiming to be tired.
Khan continues to act suspiciously, refusing to be drawn on any details of his past or why he was on the Botany Bay. McGivers visits him, admitting her interest in him - something Khan capitalises on readily for his own advantage. At a lavish dinner Kirk sits back whilst Spock and McCoy gently needle Khan about the Eugenics wars, pointing out that the genetically engineered super-humans who were created had been dictatorial tyrants. Khan argues that had they succeeded Earth would have been united under one leadership, "as Rome under Caesar", a prospect he clearly considers to be quite tempting. When Kirk enters the conversation Khan inadvertently says "we" in reference to the supermen, revealing where his loyalties lie. Khan excuses himself and returns to his quarters.
Subsequently Khan pressures McGivers into helping him take the ship, which she reluctantly does. He beams to the Botany Bay and wakes his people, transporting them back to the ship where they take control. The bridge is locked off and life support shut down, rendering the officers there unconscious.
With the crew captive, Khan threatens to kill Kirk by putting him in a decompression chamber and sucking all the air out of the rest do not co-operate. They refuse, but before Kirk can be killed McGivers has a change of heart and knocks the guard out to free him. Kirk goes to engineering and releases tranquilliser gas throughout the ship, knocking everybody out - except Khan, who manages to reach engineering. The two fight, and Kirk manages to defeat Khan.
At a subsequent hearing, Kirk ponders what to do with Khan and his people. He is unwilling to simply let them rot in jail, and offers an alternative; he can deposit them on the nearby Ceti Alpha V, an uninhabited world which is rather bleak, but survivable. Kirk notes that the original Botany Bay criminals had gone on to tame a continent and build a thriving society, and wonders if Khan might be up to taming a whole planet. Khan agrees, quoting Milton's phrase that "it is better to rule in hell than serve in heaven." McGivers chooses to remain with Khan rather than face a court martial. Spock muses that it will be interesting to return some day and see what crop might spring from the seed colony which Kirk has planted that day.
But almost as interesting as Khan is a character often overlooked in the episode... McGivers. I don't think she is what she seems at first, simply a weak person who Khan forces to help him. In her conversation with Kirk about men of the past, she's practically drooling over the idea of a big strong man with an overwhelming personality. She openly admits that she finds such men attractive. It's not so much that Khan "conquers" her as such... rather, Khan just happens to be the type of man she wants, who is acting as she has always wanted a man to act.
There's a deleted scene in the original script that expands on this; a friend of McGivers tells her that a guy is interested in taking her to a dance, and McGivers responds that he can go to hell, as she is waiting for a man who will "knock down my door and carry me to where he wants me." She is a woman who wants to be conquered by a manly man - she's just the sort of person Khan wishes everybody was, in fact.
And yet she's also conflicted. Khan represents everything she has always wanted from a guy... but to have him, she has to betray everything and everyone she knows. She talks herself into it, only to find that the taste is rather bitter in her mouth - too bitter, when Khan starts to line her shipmates up to die.
And yet even though she saves Kirk, she has already burned her bridges. There's no way she could reasonably go back to being a regular member of the crew, even if Kirk were willing. The trust would be gone. So in the end, she is left with no choice but to do what she wanted to do in the first place. It's an interesting little arc for somebody who is a minor one off character, especially given that it is rather overshadowed by Khan in most people's eyes.
You have to somewhat question how Kirk acts here. Surely McCoy told him that Khan's first action on waking was to threaten him with death. He's very obviously withholding information about his past. Yet Kirk allows him free access to the computer library, including the engineering details of the Enterprise itself. How dumb is this? And of course, without it Khan would likely never have been able to take over as he did. Poor show by Kirk. Their needling of Khan into revealing his loyalties was so well done, it's such a shame that they didn't do anything about the suspicions they had.
Of course you can't watch this one today without being aware of what it led to. Ceti Alpha V was blitzed when the next planet out exploded six months later (why on Earth does a planet just explode one day, anyway?), and Khan and his followers were barely able to survive. Indeed McGivers didn't survive. That led to Spock's death, the creation of the Genesis planet, Kirk's exile to Vulcan, the rebirth of Spock, the death of Kirk's son, the saving of Earth from the Cetacean Probe... this one event shaped a good deal of Kirk's future!
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