At an opera house, Moreau and his men plant an explosive device that destroys the building. When Peter, Olivia and Ella & Astrid arrive to inspect the wreckage, they discover Moreau's device intact and assume that the bomb must have been a dud. At Fringe HQ in Boston, Peter's attempts to deduce the device's function prove unsuccessful, and he concludes that only Walter is smart enough to solve the mystery.
Peter visits his father, who has been imprisoned for life after standing trial for the role he played in the universe's degradation. Peter explains to the dishevelled Walter that a wormhole which opened in Central Park was emitting radiation, prior to being sealed in amber. Walter observes that the wormhole would only emit radiation if it was a gateway through time, and Peter affirms that the carbon levels were consistent with the late Palaeozoic Era, 250 million years ago. Peter shows Moreau's device to Walter, explaining that the End of Dayers use these bombs on 'soft spots' to accelerate the disintegration of the universe, but Walter decrees that he cannot examine the device without his tools and instruments.
At the lab, Walter struggles to determine the device's function. He recalls the day that they activated the machine, observing that the two universes are inextricably linked, and that by destroying the 'rival' world, they have also doomed their own. When he asks about Walternate's current whereabouts, Peter reveals that their old foe has become a recluse. Walter thanks Peter for speaking on his behalf at his trial, but Peter reminds him that he was the one who got into the machine and destroyed the other universe, telling Walter, "No matter who's at fault, you're my Dad".
That night, at home, Olivia and Peter discuss having a child, but she refuses to bring a baby into this dangerous world. In the morning, Walter calls his son, announcing that Moreau is splitting atoms. He explains that each canister contains residual traces of a radioactive isotope, which will leave a signature by which they can track Moreau. Following the radiation readings to a camp ground, Peter finds no trace of Moreau or his weapons, but discovers a special key. Meanwhile, in Central Park, Moreau deposits a bomb at the amber. After the terrorist is identified by a witness, Olivia and Elle head off in pursuit. However, shortly after they arrive at the park, a blinding light knocks them, and the entire Fringe team, unconscious, tearing a whole in the amber.
Later, Olivia's friends and family - including a heartbroken Peter, Ella, Broyles, Walter and Nina - attend her funeral. On the way back from the service, Walter has a brainwave and demands to be taken back to his lab. After a night of experiments, Walter visits Peter and claims that they can save both worlds. Walter reveals that he now knows how the pieces of the machine came to be buried underground, so far in the past - he sent them back through time, using the Central Park wormhole. He explains that to save both worlds, Peter needs to make a different choice back in the past, when he entered the machine. They plan to bring Peter's consciousness forward in time, so he can witness the future and change his actions accordingly. However, both acknowledge that the cost of changing time could be high.
Released from the machine, Peter announces that he knows now what the machine is capable of and where it came from, revealing that they themselves as the First People deposited the machine in the ancient past. He reveals to the two Fringe divisions that their worlds are inextricably linked, and that they must now work together to fix the problem. However, Peter suddenly vanishes, with no-one in the room acknowledging his absence. Walter and Walternate begin to argue, but Olivia tells them they need to work together to fix the problem.
Outside Liberty Island, the Observers stand and watch. The lead Observer - September - tells his accomplice that none of the Fringe team remember Peter, because he never existed. September announces, "He served his purpose".
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