At the Department of Defense, Olivia gets a checkup after eight days back with Fringe Division. She feels fine. She and Walternate discuss the "other" Olivia Dunham's ability to cross between universes. He wants to run experiments to see if she can cross too.
While getting dressed, Olivia gulps a red pill. Peter appears in the closet mirror and says pills won't help; he's not going anywhere. He again informs her that she is NOT this world's Olivia. He knows she doesn't feel fine . . . and she can't ignore him.
In the subway tunnel below a quarantined Brooklyn bank, two men cut a chunk from the quarantine amber and carefully open it to reveal another man, who looks exactly like one of them. As they revive the guy, smoke from the cut amber trips an alarm, and more amber smoke grabs one rescuer. The other flees, carrying his look-alike.
Surveying the scene, the Fringe team assumes it was an attempt to steal valuables from amber victims. Charlie plays a video he watched recently, about the development of Amber 31422 as a quarantine element. It shows this same tunnel as it was four years ago, and they realize that there's a new guy in the amber: the thief, caught during the reseal. Lincoln picks up a piece of the cut amber bearing the impression of a face. This guy wasn't after purses.
Walternate meets with Colonel Broyles. He somberly recalls developing amber and laments that hundreds have been trapped since its first use. If people knew that the victims can be removed and revived, he says, it would cause a revolt. Broyles, surprised by this revelation, promises to find the tunnel guy. Walternate adds that Olivia's tests will be stressful. Broyles will keep an eye on her.
The team IDs the amber guy as Joshua Rose, a bank robber from a Fringe case four years ago, who used a device to access vaults without setting off the alarms. (Just like Mitchell Loeb in Olivia's world.) Since it also caused molecular degradation, they had to quarantine the half-dozen areas where Rose pulled jobs. At the Brooklyn bank, Rose got caught in the quarantine. Broyles explains about amber people being in suspended animation, not dead.
Elsewhere, Rose recuperates in a hospital bed, tended to by his look-alike.
Searching Rose's old apartment, Olivia finds a picture of twin brothers. Lincoln says that Joshua's brother, Matthew, is an accountant who cooperated with the previous investigation. Charlie finds a secret room containing equipment and gas canisters, which could be used to build a "negative matter ring" that can weaken a wall's atomic structure. Olivia hears a faint whirring sound - and they bolt as the place EXPLODES!
Matthew Rose tells Olivia and Lincoln that his brother's crimes hurt people, and others judged him because he looks like Joshua. No, Joshua wouldn't contact him, even if he could. But after they leave, Matthew heads inside . . . and talks to his brother. He says to him, you came to the bank to stop me, and I ended up stealing your life, but you're free now. The amber guy is Matthew! And the free brother is Joshua!
At the lab, Olivia plunges into the isolation tank. Hours pass. Nothing happens. Walternate has Brandon increase the drug dosages, and suddenly Olivia's on the Other Side, startling a boy at Liberty Island gift shop before disappearing. Yanked out of the tank, she gasps that she went somewhere. Delighted, Walternate says she crossed over.
Back at Olivia's apartment, Peter says that Walternate knew she could cross over, because it's how she got here. Olivia's mom arrives, concerned because she missed their lunch date. Later, she tells Broyles that Olivia hasn't been herself.
After Peter tells Olivia about identical twins at his high school, she dashes to HQ and tells Broyles that the Rose twins switched places. Matthew wasn't angry about Joshua's crimes; he was ashamed. Because he's Joshua. Although a retina scan confirms that Matthew is Matthew, Olivia is still suspicious.
It turns out that Joshua's planning another heist, but Broyles orders Olivia to go home. Instead, she gets Farnsworth to determine what banks Joshua might hit if he wanted to avoid hurting people. Soon, Olivia finds Joshua's device below a Bronx bank - and he knocks her out from behind.
Fringe team arrives and counts down to quarantine. Matthew shows up and climbs through the hole in the vault wall. Charlie and Lincoln drag Olivia out of the tunnel. Matthew confronts Joshua, whose real plan is to sacrifice himself, so no one ever knows Matthew survived the amber. Twenty seconds to quarantine! Matt runs out, and Joshua is trapped.
Later, Olivia visits Matthew and again accuses him of being the man trapped in amber. But she just leaves. Peter says she let Matthew go because she understands his situation: Trapped in amber, like she's trapped Over Here. He explains that, since he's in her head, he knows things . . . and so does she. Like that the Twin Towers have fallen, her sister Rachel's alive, and her niece Ella was born. Today is Ella's seventh birthday, in fact. Olivia says there's no way to prove it. But there is.
Olivia goes into the tank and back to the gift shop. Looking out a window, she sees that the Twin Towers are gone. Then she calls Ella, who knew Aunt Liv wouldn't forget her birthday. Olivia knows the truth! In the lab, Brandon and Walternate haul her out of the tank, but she says it didn't work. "All I saw was black."