John is meeting with a therapist using hypno-therapy to get into his background, but John's amnesia is impenetrable. She prescribes some medicine but John is less then satisfied. Meanwhile at a garbage dump, a homeless man wakes up and finds himself next to the attractive legs of a woman…who has been cut and half and only the lower half remains.
Frank Hayes is interviewing the homeless man and Avery isn't happy with the lack of ID. They eventually check the DNA and find another homeless man, Daniel Bowen, is responsible. But he's at a clinic and has an airtight alibi – he was locked up the night of the murder.
At The Sea, John is testing Digger's patented hangover cure (he's depressed –they think he's hung over) and proving his knowledge of bar drink ingredients. Karen and Digger try to convince him to get a day when Frank shows up to get his input on the new case. They check out the Saybrook Clinic where Bowen is, which was founded by a Dr. Matthew Jansen. They confront Jansen, who is skeptical and refuses to cooperate, invoking doctor-patient privilege. Jansen is an expert in repressed memories, which perks John's interest, and he refuses to let the police talk to Bowen as he is in the middle of treatment. Frank has a court order and overrides him, but Bowen isn't talking. John notices scars on Bowen's arms and he talks about using a butcher knife in the cafeteria and how he hurt someone, but he couldn't have. Bowen claims he can leave the room…in his mind. John notices Bowen has a problem with his leg that would have made it difficult to haul a body, but John notices Bowen saying something about a brother and John suspects an identical twin is involved, explaining the DNA match.
John pins down 18 unidentified births of possible twins and with the aid of Stella the police researcher track it down to a single pair of twins – Daniel and Christopher. They get an address on Christopher and Frank and John head out to meet with him. They meet with a female janitor who tells them Christopher has been dead…for nine months.
Talking with the woman, Polly Kendall, John determines that she works with a plastic surgeon and notices several tell-tale clues indicating she has male traits. She's a transsexual and is actually Christopher, the "man" they're looking for. She flies into a rage and they take her in along with her brother, but they're stumped. Frank runs Jansen's record and finds he has a prior crime for violence against someone interfering with his treatment. Meanwhile John gets back to The Sea to find Karen holding a speed date meeting to get John involved in dating. It doesn't go well and the one woman John has a connection with he puts off with a long spiel of his made-up background.
John meets with Jansen who talks about his theories of resurrecting the past to help cure his patients. John mentions he has amnesia and Jansen is intrigued, offering a cure. He shows John his sensory deprivation chamber which lies at the heart of his treatments. John agrees and begins to get visions of his memories of his previous adventures since "waking up," then a desert, then himself swimming. John snaps out of it and then panics, trying to get out of the deprivation chamber. Finally a guard lets him out – two hours have passed and Jansen has disappeared along with the tape of the session. John does find Bowen's session-tape and takes it to Frank. Then they get word of a new kill – the top half of a victim. They review the Bowen tape and Frank suspect Jansen may be acting out his patient's memories. They also check the victims' histories and determine that they were working with Child Services when the Bowens were separated as children. They go to the now-abandoned Child Services' building and find the missing halves of the two bodies, crudely put together.
Both victims were on the administrative board that dealt with the Bowens, but there's a third administrator Druzinski and he's out camping where they can't find him. Polly is released and John notices that she is missing a fingernail. John goes to Jansen's assistant Elizabeth Miller and reveals where he thinks the next victim is and that Bowen is being released.
Out in the woods, Miller approaches the camp site and goes toward the tent with a butcher's knife…and stabs the man inside. John steps out from behind a tree and goes after her when she runs. She leaves by truck and John is forced to pursue on foot when his car is blocked off by an RV. He finds a nearby hang glider and buys it from the owner and goes off after Miller. Landing on her truck, he manages to knock her off the road.
The police bring Miller in and John reveals that he noticed Miller had the same missing fingernail as both of the Bowens – she's their mother. She gave them up as a kid but then realized they were separated and decided to get revenge on the ones who separated her children. Miller denies having anything to do with the disappearance of John and his psych tape and Frank pulls off John when he confronts her. John doesn't believe she's involved with Jansen's disappearance.
Later Polly and Daniel are reunited at a new mental health facility, and John is at The Sea and decides to approach the woman he kind of hit it off with during the speed-dating. This time he tries honesty and they start to bond. Meanwhile mysterious men bury Dr. Jansen in the desert…men employed by the mysterious Yellow Teeth, who has John's therapy tape.