No idea where this came from. This really isn't the way I see Sheppard, there may be aspects of his character that are similar, but I don't think this is him, at least not the him we see in canon. Consider this an AU John if you wish.
Many thanks to kitkat3979 for beta.
Sometimes, John forgets.
He forgets that he isn't the nice, charming, easy-going guy everyone thinks he is.
There was no guilt when he pulled the trigger and ended Sumner's life. It was the only viable course of action.
The Genii soldiers were nothing more than obstacles to be rid of.
Sometimes, John lets himself believe.
His family had known the real John, but his mother had refused to see it until it was too late. His superiors in Afghanistan had caught a glimpse of it, and so did the General who exiled him to Antarctica. But not Weir, or Teyla, or anyone else in Atlantis except maybe Rodney McKay, who despite their friendly banter, never calls John by his first name. He's keeping his distance.
Atlantis knows, without a doubt. Which is why she responds to him. Their thoughts are the same.
It's also why Carson was afraid of her.
Carson should be afraid of him too, but all he sees are smiles, jokes, and heroics.
John isn't a hero.
Sometimes he wonders if anyone in Atlantis has any idea what they have in their midst, but he quickly dismisses that line of thought and plasters on a grin or a smirk for the next person passing by.
Sometimes, he catches Rodney looking at him, and John wonders how much that genius brain has figured out.
Sometimes, John imagines Rodney coming to him, and telling him, "I'm not afraid of you, John. I'm afraid for you.