The episode brought us two stories - now slightly intertwining, soon to be more - the shapeshifters and Peter, both of whom have returned.
Dr. Truss used to work for Massive Dyamic, until Bell put an end to his research. Truss's work was in cell regeneration, or the science at the basis of shapeshifting. In terms of his genius, belief in his own work, but guilt when things go wrong, Truss is in many ways another version of Walter.
The real Walter has his hands and mind and heart full, as Peter, now in Fringe Division custody, asks Walter to help find out what happened to him. On the way to his first meeting with Peter, Water hypothesizes that this could be a third Peter, from yet another (third) alternate universe. Olivia refutes the hypothesis, pointing out that it wouldn't account for why she had been seeing Peter's face in her dreams. And we viewers of course know that this Peter is our Peter - that is, the Peter from last year's alternative universe (the alternative universe of all seasons thus far), whom Walter kidnapped/saved as a boy.
In one of the most touching scenes ever seen on Fringe, Peter pinpoints in his conversation with Walter just where and when the new reality - without Peter - came to be: the Eternal Bald Observer did not save Peter when he fell through the ice all of those years ago. Yet he - our Peter - is back now.
Walter, for all his genius, still can't quite accept this. His heart tells him this is the Peter he raised, and knows as an adult. His brain tells him this too. But the guilt he still feels for breaching the two universes, and losing Peter in the water anyway, blocks his coming to terms with Peter's return now. But give him time.
Meanwhile, Peter is making his customarily excellent contribution to the Fringe team, helping them in their attempt to understand the shapeshifters. But we'll need more than understanding to beat them. Their agent has now transformed into someone working in Fringe division, and - guess what - they're under the likely direction of Walternate, or someone from the alternate universe that communicates with ours via clacking typewriter.
Kudos to J. R. Orci and Graham Roland for writing a really memorable episode.
... Fringe 4.2: Better and Worse Selves ... Fringe 4.3: Sanity and Son ... Fringe 4.4: Peter's Back, Ectoplasm, and McLuhan