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There is a singular moment where the Doctor nearly lets this happen. This body is new, has never been touched like this, and it feels--good.
He trusts Amy not to make this a Thing--it could be safe, no one would have to end up hurt. She's a kiss-o-gram, Rory couldn't possibly mind a teeny tiny dalliance.
But then his brain catches up, spoiling all his fun. This is little Amelia Pond--fairy tale Amelia Pond and he is not her knight in shining armor (not that Amelia Pond needs one). He can't, really doesn't want, to do this.