Hi,
I'm looking for a fic where John is missing. There is a John in Atlantis, but he's not real...I think he may be part replicator? He has nanites that make everyone believe he's real. Then he dies. Then they find another John off world and bring him back thinking it's the real one, but it's not. I think they find one more fake John before they find the real John, but by this time they don't believe he's real either. They put him in isolation and he doesn't understand why. In the end it's Elizabeth who realizes that he's real and how much they are hurting him.
Does anyone know this story?
Thanks
Found!! by 
saphirablue. It's Heartbeat by Stealthdragon.