Fringe/Recap/S02 E21

Season 2, Episode 21:

Northwest Passage
Peter is on his own, hiding from the FBI and travelling aimlessly through Washington State, when he stumbles across a murder in a small town that bears all the hallmarks of a Fringe case. He offers his services to the local sheriff's department in solving what quickly becomes a spree of killings. At the same time, he becomes convinces that Newton and the Shapeshifters are following him and are somehow responsible for the killings.

At the end of the episode, the killer is discovered to be a mentally disturbed man living on an abandoned dairy farm, and Peter comes to think that him seeing Newton is just a stress-induced hallucination, until Newton appears in his motel room and puts a gun to his head. The "Secretary" is there too, and he is revealed to be Walternate -- Walter Bishop, Secretary of Defence, and Peter's real father.