Since the series was cancelled, the execs gave out the secret at a press conference:
“Gail Berman, president of Fox Entertainment, revealed the secret of the network’s canceled SF series John Doe to Zap2it. The series, which starred Dominic Purcell as a man who knew everything except who he was, ended before uncovering the secret of his abilities.
But at Fox’s fall press preview this week, Berman told the site that she had discussed Doe’s underlying premise with creators Brandon Camp and Mike Thompson. The secret: Doe was just a regular guy. “[According to the show], when you’re very close to death, when you’re seeing the white light, God or a higher being gives you all the information of life to carry on to the next life,” Berman said. Doe was about to die, but for whatever reason, he lived after being imparted with that knowledge, she said. The shadowy people who were after Doe knew what happened to him and were trying to keep him from discovering it himself, Berman added.”
This does not make sense to me. If Fox hadn’t cancelled the series and the story played out according to the above explanation, I think many people, including myself, would have been very unhappy.