season 2
In the episode "The Man from the Other Side", Walter decided he had to let Peter know the truth, but, as he was about to explain, they were called in to investigate a case. They discover that Newton is attempting to bring something -- or someone -- from the other universe into our world. The sonic vibrations released from Newton's device would inevitably kill anyone from this universe. Peter, when attempting to foil Newton's plan, unexpectedly finds out that he is in fact, not from our universe. He is injured and while in the hospital, confronts Walter ("You said the effects of Newton's vibrations would be devastating. And they were, they...destroyed that FBI agent, they just...disintegrated him like he wasn't even there. But they didn't kill the man from the other side...and they didn't kill me. I'm not from here, am I?") and angrily blames Walter for his mother's (from our universe) suicide ("That's why my mother committed suicide, isn't it? She knew. Didn't she? And when I left, the guilt was too much for her to live with...the lie.") At the end of the episode, Olivia notifies Walter that Peter had checked out of the hospital and is now on the run to resume his isolated and nomadic pre-Fringe life. Despite attempts to track him down, Olivia is unable to locate him.[5]
http://en.wikipedia.org/wiki/Peter_Bishop