In an attempt to distract himself from Peter's recent disappearance, Walter goes on a drug trip and concocts an elaborate fairy tale for Olivia's young niece, Ella.
Walter's story revolves around a private detective named Olivia Dunham who takes the case of a missing person named Peter Bishop.
Olivia goes to visit Lieutenant Broyles at a piano bar, and shows him a logo that she found in Peter's apartment. Broyles tells her that the logo belongs to Massive Dynamic. Olivia then meets with Nina Sharp, who warns that Peter is a dangerous con man and is probably up to no good.
Olivia calls Peter's sweetheart, Rachel, and hears signs of distress on the other side of the phone. She rushes over to Rachel's house, but it's too late...Rachel's heart has been surgically removed from her chest.
At the scene of the crime, Broyles tells Olivia that Rachel was not actually Peter's sweetheart, but instead a hired actress. He then tells Olivia to back off her investigation. Olivia leaves, but not before swiping Rachel's datebook.
Inside the datebook, Olivia finds a check from Walter Bishop, a mad scientist responsible for inventing bubble gum, rainbows, and singing corpses. Olivia meets with Walter, who explains that Peter was his trusty lab assistant before he disappeared one night along with Walter's magical "glass heart."
In the parking lot, Olivia is attacked by a man who wields the same type of laser weapon that was used to kill Rachel. Olivia does a little research, and finds out that the weapon was patented by Massive Dynamic.
Olivia confronts Nina Sharp about the weapon, and Nina explains that one of her prototypes was stolen by a group of men called "The Watchers." Olivia follows Nina back to her house, and eavesdrops on a conversation she has with William Bell via the window to the other side. Nina tells Bell that Peter is in possession of the glass heart, and if they can acquire it from him, they will be able to create a portal between universes and finally reunite.
Olivia is knocked unconscious. She awakens on a boat, where Nina Sharp and one of The Watchers seal her in a coffin and toss her out to sea. Olivia is saved just in the nick of time by Peter, who takes her back to his hideout.
While at the hideout, Peter explains to Olivia that Walter is not what he appears to be, and that he is only able to create such wondrous things because he has been robbing children of their ideas. Peter then reveals to Olivia that he was born with the glass heart, and had originally given it to Walter, but he decided to take it back after discovering Walter's ugly secret.
Peter's hideout is invaded by Watchers, and they steal the glass heart right out from Peter's chest. Olivia saves Peter by wiring him up to a few batteries, but this is only a temporary fix. She tells Peter that she knows who has his heart.
Olivia and Peter burst into Walter's lab and find him holding the glass heart. Peter takes it from him, and Walter pleads that he can change his evil ways if given a chance. Peter walks out, leaving Walter all alone.
At this point, Ella pulls Walter out of the story, and tells him that all good fairy tales end with, "They lived happily ever after." According to her ending, Peter decides to forgive Walter, and then he splits the glass heart in two so each of them can have a half.
Walter tells Ella that he approves of her happy ending. Olivia walks in, and tells Walter that she hasn't had any luck in finding Peter.
Outside the house, an Observer watches Walter. He calls one of his colleagues and reports back that he is concerned because Peter has not yet returned.