In my mind, he was exactly who he appeared to be -- the fourth Doctor, aged and infirm. Somehow, in some way, he retired and grew old like his old mentor, Professor Chronotis. I don't know if he was from an alternate timeline. Don't care, really, especially since I doubt we'll ever see him again.
He's a character for the fans. Like Wormhole
says, he's who we want him to be.