Peter is still being held by Fringe Division who have yet to fully trust him, so when a pattern of tragic time loop anomalies emerges, the team begin to wonder if Peter's unexplained appearance is responsible. Meanwhile, Walter still doesn't believe that Peter is his son, and Peter attempts to explain his relationship with his Olivia to the Olivia of this timeline.

In an effort to find a way home, Peter journeys to the Alternate Universe to confront Walternate. The venture proves more dangerous than expected when Peter finds himself unexpectedly thrust into the conflict posed by the human shapeshifters. Meanwhile, Olivia receives a dire premonition from the Observer, September.