Warning: major spoilers ahead. Read at your own risk!
In Rye, New York, a man living in a quaint neighborhood enters his home, limping heavily before passing out completely. When he awakens, he's strapped to a table not unlike one of Dexter Morgan's hopeless victims, watching as a stranger operates on his body. Some undetermined time later, the police arrive in response to a 911 call — they discover the man's body with its heart carved out. Their understandable first impression is that the man is dead, but they're in for a rude awakening themselves when the victim's eyes burst open.
"Don't -- don't let me die," he whispers. Elsewhere, the surgeon walks away with a cooler in hand. Three guesses as to what's inside.
Later, Olivia Dunham returns to work for the first time since coming back from the mysterious world of Over There. She recalls her experience during a conversation with Broyles, who remains visibly disturbed from seeing his alternate version's mangled corpse some days earlier. Olivia does her best to console him by describing the Broyles she met: an honorable and committed man who feared for his family's future. Broyles seems genuinely moved when he learns that his double had a son and daughter and was very close to his wife — things that Broyles desperately wishes he was able to have for himself.
Broyles and Olivia aren't the only ones with dilemmas, as Walter Bishop tries to coach his son into telling Olivia the truth about his romantic affair with Bolivia. But unlike his father, Peter's first instinct is to tell Olivia the truth, no matter how difficult it is on either one of them. He isn't prepared to tell her right away, however, especially not when Olivia appears on the field, surprising everybody around her. With the gang back together, Olivia and the Fringe team investigate the case of the man with the missing heart. They learn that he died only three minutes after his apparent resurrection, and Walter notices that the man had had heart surgery at some point prior to his grisly death.
Olivia and Peter go to see the surgeon who operated on this patient, but when they learn that the doctor needs a few minutes, Peter sees an opportunity to tell Olivia the truth about his relationship with Bolivia. It's a difficult moment for both of them as Peter tries to break the ice gently and Olivia does her best to understand, but despite her words, her face betrays the hurt inside. But they're on the clock, and if there's anyone who can put emotions aside in favor of work, it's Olivia. She insists it's all right and moves on with the job.
But it's not all right. Later that night, freshly showered and warm in her apartment, Olivia can't help but feel the stink of Bolivia all over her belongings. She tries to do the laundry, but Bolivia's forgotten a clean load in the dryer. Going through the contents, Olivia discovers one of Peter's T-shirts, and she can't take it anymore — the hurt is just too much to bear.
The next morning, Olivia runs into Astrid Farnesworth at the Federal Building in Boston. After asking her colleague and friend some uncomfortable questions about Peter and Bolivia's relationship, Astrid quickly reassures Olivia that everything Peter was feeling was intended for the real Agent Dunham. "Whatever feelings that Peter had weren't about her," she says. "They were about you, and they were real. They still are."
It's not enough of a consolation for Olivia, who continues to carry the burden of Bolivia everywhere she goes. As the investigation progresses, Walter believes that the organ thief is trying to show mercy towards his victims. Furthermore, he deduces that the thief is stealing all of the organs from the same donor, going one step further by offering a bold hypothesis: the thief is trying to resurrect the donor. Sure enough, at the thief's hidden lair, we see that he's reassembled a young female cadaver and has her strung up to strings, manipulating her body through the air like a marionette — suddenly, the episode's title makes sense. He weeps quietly as he watches his sad, deceased cadaver dance through the music.
The team works to narrow down the culprit and out of a pool of possible suspects, Peter believes he's found the guy. But Olivia, an expert in profiling, quickly pooh-poohs the idea and says that whoever is trying to resurrect this girl is someone who is desperately in love with her. The words hang heavy in the air, and the already thick tension between Peter and Olivia grows even thicker.
Eventually, they're able to apprehend the thief, but only after he successfully reanimates his long lost love. But the woman he brings back to life is not the woman he knew: she's virtually soulless, staring back at him with glazed over eyes and a faint moan in her throat. There's nothing of the woman he knew still there, as he explains it to Olivia upon his capture: "I don't know what I brought back, but I know that it wasn't her."
The confession weighs heavily on Olivia for at least two reasons. The first reason surfaces during an end-of-episode confrontation with Peter: although she understands the facts and gets why Peter believed Bolivia's ruse, Olivia says that her feelings for Peter were the only thing that got her through her struggle on the other side; she held onto him despite the fact that it wasn't reasonable or logical. "So why didn't you," she demands. Even though Bolivia is gone, she remains everywhere, her presence hanging over her clothes, her job, her apartment and even on Peter.
"She's taken everything," she declares, walking away from Peter and leaving him to stew in the lingering outburst. But despite her harsh words for Peter, Olivia must recognize a second irony in the organ thief's confession: just as the girl he reanimated was not the same girl he knew when she was alive, Olivia is no longer the same person she was before her abduction in the parallel universe. The only question is, can Olivia come back from the brink? Time will tell.
In the meantime, it appears that something very important is on the horizon, as an Observer quietly watches Peter and Walter Bishop going for a late night snack. The Observer makes a phone call and ominously tells the unrevealed person on the other line: "He's still alive."