Olivia uncovers a dangerous force that may be connected to Walter's past experiments with the drug Cortexiphan. Their investigation forces Walter to leave the lab for the first time in years as he and Olivia head to Massive Dynamic in New York to examine old case files. Walter struggles with life outside the lab as he confronts the demons of his past.

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.