John liked people to drop their guards around him. It's why he was so laid back, why he didn't like people to know he was a member of MENSA, it's why he never bothered to tame his hair. But even though he played the part of the eternal youth, John noticed things.
He noticed the way sometimes Rodney would stare off into space, tapping idly against the table, tap tap-tap-tap. Completely unaware of anything around him, completely engrossed in his thoughts.
He noticed the fob watch laying haphazardly in Rodney's drawer and when he'd asked about it Rodney had hardly looked at it before stating dreamily that it didn't work, and never had. He'd asked why he didn't fix it and Rodney just muttered that he just hadn't.
It wasn't long after he'd found that watch that something had shifted in Rodney, and he was the only one who noticed it.
When someone, anyone, denied him anything there was a dangerous glint in his eye that reminded John of murder, and he couldn't fathom why. When Zelenka died in the lab accident, though, John denied the look of smug satisfaction he'd noticed on Rodney's face.
He noticed the way Rodney touched him, each and every time. It was hesitant, almost gentle, but never loving. And he knew that it was because no matter what, John was always, would always be, second best. And when Rodney asked him in silky, affectionate and threatening tones to call him Master when they made love, he thought of Zelenka and Carson and how much he missed them, and how much he'd always wanted Rodney but god not like this. And he'd muttered "yes master." and Rodney-Master was kissing him like a two cent whore.
Rodney liked to stay up till all hours of the night and draw up plans and tinker. When John would come and try to coax him to bed, or ask him what he was working on, Rodney would snap at him and tell him to go to bed, go away, just let him work in peace and that even if he were to explain everything to him, John still wouldn't understand. And he would usually sleep alone, defeated and lonely and wondering what the Hell happened to the Rodney he used to dream about.
There were mistakes, lab accidents, and people were dying so often John had taken to wearing black at all times. And if he was the only one that noticed all the deceased had offended or hindered Rodney somehow, well, he wasn't going to point it out to anybody.
Some nights Rodney would come to bed clutching his head and muttering that the drums needed more than this and he just didn't have the patience anymore and why the fuck bother, anyway. The Doctor was dead and what use was the universe without the Doctor in it. And John didn't know if he had meant Carson or some other doctor but it hurt just the same.
He had seen it coming months before anything happened. As it turns out, he wasn't the only one who had noticed the changes in Rodney. And when Elizabeth had approached him to ask him for his help, he'd nodded and told her he would do what he could and not to worry. Then he went to the labs and told Rodney what Elizabeth had said and he hardly blinked. Told John to go back to the room, go to sleep, and he'd turned on his ipod and tapped his foot to his own internal beat while singing to Goldfrapp and building what looked oddly like a transmitter. And three months later when the Wraith came he wasn't sure if he should defend Atlantis or throw Elizabeth toward the Wraith queen. Because if there was one thing he'd learned about this new Rodney it was that he liked things to be dramatic and extravagant, and that he really, really didn't like Elizabeth.
He noticed the excited gleam in his eyes when they approached Earth, seen the look of utter joy that spread on his face when he made the world wide announcement.
"People of Earth. Hello again, I'm sure you don't remember me. How could you?" He laughed, and changed his tone. "Its been a very long time, and you've been very naughty. There's no one to save you anymore, and isn't that a shame. Its your own fault, though. If you hadn't killed him, maybe I wouldn't be here now."
And as the planet Earth gaped in bewilderment and fear, John watched Rodney's face and wondered how long he had been like this, and realized that it didn't matter.
"Look at it Colonel, isn't it wonderful?" And John nodded mutely as he watched the Wraith ravage his home world.
"Yes Master. Wonderful."
FIN.
If you didn't get from the two lousy hints in the story, the Doctor is dead here. The human organizations finally caught him and dissected him and did god knows what else.