Fringe/Recap/S03 E09

Season 3, Episode 9:

Marionette
The Fringe team investigate when the recipient of an organ transplant is found in his home, still alive despite the organ -- a heart -- having been removed. They discover that more organs have been stolen from recipients, and that all the organs came from the same donor, a clinically depressed young woman who committed suicide. Walter theorises that the thief is experimenting with techniques that he and William Bell worked on in the field of reanimation, and eventually Olivia and Peter figure out that the thief was part of the donor's support group and that he is attempting to bring her back to life. Fringe Division tracks him down and arrests him only moments after the thief succeeds in reviving the donor, but he's distraught when he realises that despite having brought her body back to life, she's just an empty shell and not the woman he fell in love with.

Meanwhile, Olivia is adjusting to life after her return to the prime universe. At first she's overjoyed to be back with Peter and Walter, and to have some of the little things that aren't in abundance in the alternate universe (like coffee). However, Peter soon reveals the truth to Olivia about his relationship with Fauxlivia.

"Peter: I noticed... changes. Small changes, but they were definitely there. She's much quicker with a smile and less... I don't know. Less intense, maybe. She said that when she was over there, what she saw of her other life, it made her want to change, to be happier. And I believed her, because that made sense... And so I came back for you. For us. And we started seeing each other. And I explained away the differences because our relationship was different. I thought she was you, Olivia."

Olivia claims that she understands, but later she has a Freak-Out in her apartment when she tries to wash all the clothes Fauxlivia wore and the sheets she slept in, and realises just how thoroughly Fauxlivia infiltrated her life. At the end of the episode, after arresting the organ thief, Olivia tells Peter that even though she can logically comprehend how Fauxlivia took her identity, she can't understand or forgive Peter for not seeing through the deception.

"Olivia: She wasn't me. How could you not see that? Now she's everywhere. She's in my house, my job, my bed, and I don't want to wear my clothes anymore, and I don't want to live in my apartment, and I don't want to be with you. She's taken everything."

Later, Walter and Peter go to get a milkshake together while September the Observer watches. He calls someone and informs them that "he is still alive".