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Kirk is recording a Captain's Log after the opening scene on the volcano planet. He says the whole thing passed without incident and they weren't detected by the natives. While he's saying this it cuts between shots of the natives watching the Enterprise fly away. When Kirk's finished it shows the whole bridge crew staring at him, open-mouthed, thinking "this guy's the CAPTAIN!?" Then Kirk says "What? They barely saw us!" in a whiney voice.
Yes I read about it on wikipedia, very similar explination to the one I came up with.
He was surgically altered and had his memory wiped, I assume the wipe didnt go that well.
Although they didnt mention on wiki, I assume they did something to his blood so that he would always heal back to the Harrison form if he tried to alter himself back to how he used to look through more surgery.