Phasers to stun?
So Scotty shoots and stuns Khan in one shot when they are on the bridge but Uhura shoots him 5 or 6 times when he's fighting with Spock but has virtually no effect?
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Pretty sure Khan was faking it on the bridge
For what reason?
Makes no sense to fake it as he had the upper hand at the time, he was too strong and powerful as he demonstrated when he woke up and took the Kirk out then killed Marcus.
Watch the scene again - he didn't "wake up"; he was never stunned.
When people "wake up" in movies, they blink and look confused for a second or two - Khan just opened his eyes. The phaser had little to no effect on him
However, he'd just been double-crossed by his allies. Makes sense to "play dead" until he knows what the score is.
Once he'd figured out what actually happened, why Kirk did what he did, confirmed whose side everyone was on (i.e., not his), AND waited long enough to ensure no backup was on the way, Khan acted swiftly and decisively.
He disabled Scotty, Kirk and Carol Marcus, but left them alive to use as hostages
He killed Admiral Marcus out of revenge
Then he hailed the Enterprise