In the parallel universe, the New York City Fringe team, under the jurisdiction of the Department of Defense, is alerted about a breach in the system. The alternate versions of Charlie and Olivia (aka Bolivia) leave with the SWAT team. They're accompanied by another agent, Lincoln Lee, who uses equipment to monitor an "event." Lincoln sends his feed from the site to Colonel Broyles, who consults with the alternate world Astrid. She calculates the possible casualties, and says that the event has terminated. Astrid recommends to Colonel Broyles that they do not enact a quarantine.
At the site, Charlie finds a man whose face is covered in tumors. Bolivia and Lincoln are confused when the man has a drivers' license from our side. "Who the hell is Jackson?" Lincoln says, looking at the former President on the $20 bill. The alternate world agents do not see Walter, Olivia and two other people sneak away.
36 hours earlier: Walter watches surveillance footage of Walternate taking Peter to the other side. Walter and Olivia look at the drawing that the Observer September left, and Walter remembers that the Observer warned him that Peter must never go Over There. They must figure out how to get Peter back.
Olivia, Walter and Broyles show Nina the drawing, and she recognizes it as William Bell's technology. However, Massive Dynamic didn't build it. In the lab, Brandon explains that to cross over to the Other Side, an entity's cells need to separate and may not come back together with the same cohesion. Brandon suspects that Bell crossed over so many times that he may be degenerating. This could be the reason why he won't return to this Side. Nina says that Olivia and the other Cortexiphan kids have the ability to cross over. A number of them working together could create enough energy for it to work.
Broyles shows Olivia that Massive Dynamic has helped more former-Cortexiphan kids re-gain control of their abilities. One of them, Nick, knows Olivia as "Olive." The other two are James and Sally. Broyles brings all the subjects to a new Fringe situation room. The three Cortexiphan subjects recognize Walter as the one who subjected them to tests as children. He asks them to help save his son.
That night, James goes to a hospital and uses his powers to cure all the dying patients. Nick and Sally retreat to a hotel room and make love with all the power that their abilities have endowed them. Olivia gives her niece Ella a cross on a chain from Olivia's mother, and Olivia says goodbye to her sister Rachel, not knowing whether she will ever see her again.
Nina sends word to Bell to meet the team crossing over, but they aren't even sure he will get the message. Broyles is concerned that Olivia doesn't have a real plan once they reach the Other Side. Walter coaches Olivia, Nick, Sally and James on making their imaginations focus on allowing the universe to slip through them. James collapses as tumors start sprouting up on his face. They realize that they have crossed over, but they scramble as sirens approach. Steam rises from Sally's body.
The alternate world Fringe squad examines James' body as Walter, Olivia, Nick and Sally hide. Bolivia compares James' $20 currency with hers -- which has Martin Luther King, Jr. on the bill instead of Andrew Jackson. She scans it with a monitor, but thinks it's merely a counterfeit.
An alarm is triggered at the alternate universe Department of Defense as the Jackson-faced $20 appears on a screen. Colonel Broyles alerts his agents that the Secretary of Defense wants to see them because of what they have found.
Bolivia, Charlie and Lincoln go to DoD and meet the Secretary -- who is Walternate. He tells them that their Fringe division, which started in 1985 to handle natural environmental disasters caused by holes in the universe, is based on his writings which are actually a lie. The holes were not natural but caused by men and they lead to a parallel earth like theirs. Walternate says that those who attempt to cross over into this world are about to start a war. He orders the agents to apprehend the invaders.
Peter awakes in the alternate universe Bishop mansion, finding himself connected to medical machines that track his temporal acclimation. He has been asleep for three days. Peter gets out of bed and talks to his mother Elizabeth in the kitchen. They share a tearful hug, having not seen each other in over twenty years. She wants to hear about his childhood, and Peter tells her that his mother from his former world wasn't strong like this Elizabeth. He thinks it's his fault the mother he grew up with committed suicide.
Olivia, Walter and the remaining Cortexiphans are forced to walk across New York when they cannot take public transportation without identification. Sally stumbles, feverishly. She denies it when Walter asks if they've exerted their abilities before they crossed. Walter hopes maybe Bell can help Sally once they find him. Sally's eyes fill with blood. They make their way to Central Park, where Lincoln is waiting with police backup. Did Bell betray them? Walter and Olivia run off into the park, but Lincoln shoots Nick and then recognizes him. A heartbroken Sally forces herself to burst into flames that engulf Lincoln. Bolivia shoots at Walter in the park, but he gets away. She is summoned to where Lincoln's charred body lays.
Walternate leaves a technical blueprint for Peter. It's the same weapon in the sketch that the Observer drew.
As he walks the city streets, Walter realizes he's been shot and falls near a hospital. Olivia ducks into a phone booth and looks up Bolivia's address in the digital directory. Meanwhile, Bolivia returns to her apartment and tells her boyfriend Frank about the events of her day. Olivia watches them from the street. She's startled by William Bell, who says he did not set them up. Bell only just missed them at the park. He warns Olivia that Walter is in trouble and they don't have much time.
Walternate enters a DoD chamber. The weapon is already built.