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Season 2, Episode 16:

Peter

Walter explains to Olivia the circumstances surrounding Peter and his trip to the other side:

In 1985, Walter and William Bell are working for the US government to develop advanced technologies. They create a "viewing window" that allows them to see things happening in the alternate universe, which is decades ahead of the prime universe when it comes to digital technology and other areas of science. Using what they see, Walter and William are developing the next generation of military and household technology, but at the same time Walter is observing his alternate universe counterpart, whom he nicknames "Walternate". Walter and Walternate both have a son, Peter, who is suffering from a fatal disease, and because he has exhausted all his options in the prime universe, Walter keeps tabs on Walternate's attempts to find a cure using the more advanced science and technology of the alternate universe. Unfortunately, the prime universe Peter passes away before a cure can be found. William Bell doesn't attend the funeral, but Nina Sharp does. Walter's wife, Elisabeth Bishop, is particularly distraught over the death of their son, but Walter attempts to comfort her by using the viewing window to show Elisabeth the alternate universe Peter: their son lives on in some fashion, even if its not with them.

Using the window, Walter continues to observe Walternate's attempts to find a cure for his own son. However, during a test on one particular compound, Walternate is distracted by an appearance of September the Observer: he doesn't see the positive reaction, and by the time he returns to his work, the result has faded and Walternate moves on to the next experiment. Watching all this happen, Walter realises that now In the alternate universe, December and August chastise September, whose attempt to observe a crucial moment in history will now likely result in the death of Peter, who is "important". September resolves to correct this mistake somehow. Meanwhile, Walter finds himself unable to stand by and watch the alternate universe Peter die as well: after perfecting Walternate's cure, he decides to build a doorway to the other universe, cross over and save him. Walter's lab assistant and Nina Sharp both recommend against the idea, but he goes ahead and builds the doorway.

Walter sets up the doorway apparatus at Reiden Lake, a soft spot where the journey will be easiest, and Nina arrives to try and stop him. She goes so far as to try and pull Walter away from the doorway and they struggle, but he crosses over anyway and Nina's arm is dragged through, rendering it insubstantial. Once he's on the other side, Walter realises that the vial containing the cure has been shattered, meaning that he can't simply cure Peter and then return to the prime universe. He walks to the Bishops' house, convinces both the alternate Peter and Elisabeth that he is Walternate and claims to have found a cure that must be administered in the Harvard lab: he takes Peter and they return to the lake. As Peter starts to realise that Walter isn't his father, Walter reactivates the doorway and they return to the prime universe. Immediately upon arrival, the ice underneath them cracks and they fall into the water. They're saved from drowning by September, and when Walter comes to, September is driving them both to Harvard. He warns Walter that Peter is very important, and mustn't be allowed to return to the other side.

In the lab, Walter gives Peter the cure and saves his life. He is resolved to return Peter to the alternate universe as soon as he's healthy, but when Elisabeth shows up at the lab and is overjoyed to see her "son" again, Walter realises that he'll never be able to send Peter home.

Back in the present day, Walter explains that the Pattern, the soft spots, the conflict between universes and the "storm" that William Bell predicted are all the result of Walter crossing to the over universe and taking Peter.

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