Fringe/Recap/S03 E01

Season 3, Episode 1:

Olivia
Still trapped in the alternate universe, Olivia Dunham is forced to sit through counselling sessions in which a therapist tries to convince her that she's really "Fauxlivia", the Olivia Dunham from the alternate universe. Walternate and his chief scientist, Brandon Fayette, have been performing experiments to plant Fauxlivia's memories inside Olivia's mind and have them take over, which would effectively transform Olivia into Fauxlivia, but they haven't been working. During one experiment, Olivia manages to escape from her cell in the DOD headquarters on Liberty Island: she dives into the water and swims to New York. Once she's there, she take a cab driver named Henry as a hostage, forcing him to drive her to the theatre in Brooklyn. Unfortunately, she arrives just in time to see the quarantine protocol go into effect, and the theatre is encased in amber.

Fringe Division is mobilised to bring Olivia in, under the impression that she's Fauxlivia and suffering from a mental breakdown. Meanwhile, despite the situation, Henry begins to sympathise with Olivia when she talks about going home to Peter, and he realises that she's honestly fighting for her life -- especially when Fringe agents corner the cab at a gas station while they're refuelling. In the midst of the getaway, Olivia shoots the cap on a gas canister while hanging out the window of a moving vehicle, a shot that only Fauxlivia (a former Olympic marksman) could make: monitoring the situation, Walternate and Brandon realise that the false memories are taking hold.

Olivia directs Henry to take her to a safehouse, but when she arrives, it turns out to be her mother Marilyn's house. At first Olivia remains convinced of her story and that Marilyn died in the prime universe, but Marilyn points out that if she wasn't Fauxlivia, she wouldn't have known where the house was at all. The brainwashing takes hold and Olivia believes that she really is Fauxlivia and simply suffering a mental breakdown. When Charlie "Scarlie" Francis and Lincoln Lee arrive, they take Olivia back to the DOD headquarters, ready to complete her "recovery" and return to work at Fringe Division. Colonel Broyles questions the wisdom of putting someone from the alternate universe on his team, but Walternate assures him that Olivia is now exactly like Fauxlivia, and therefore will comply with experiments designed to figure out how Olivia can safely cross between universes.

In the prime universe, Peter finishes giving a statement of the events that occurred on the other side to Senator Van Horn, who has oversight over Fringe Division. He doesn't answer Van Horn's question, but when Peter exits the capitol building and meets with "Olivia", it's clear that the pair have been a couple since returning (much to Walter's delight): nobody suspect that she's really Fauxlivia.