On America's Most Wanted, John Walsh covers the story of missing person John Doe. He interviews John by satellite and John shows the picture of "Turquoise," the woman from the ferry. Frank and Roosevelt are checking out a crime scene of a dead private investigator who apparently died of fright and is missing a finger. Frank notices a key around the detective's neck and uses it to open a secret chamber that holds a photographic shrine to…John Doe.
Avery and Frank call in John while Stu can't figure out how the detective died. John concludes that the man was electrocuted by a series of low-voltage shocks used for torture, that went too far. Checking the detective's appointment book they find a trail that leads to his most recent appointment – Madison Park. They talk to an artist teacher and John notices the dead man in several sketches, meeting with a man in a trench coat. John determines that the Trenchcoat Man is using sign language and they head back to police HQ, unaware the Trenchcoat Man is watching them.
They figure out the detective knew sign language and they bring in a deaf police officer while they check out leads connected to the deaf. John and Stella run down leads and come up with the name of a Charles Gitteau – the name that matches the assassin of President Garfield. They track down his address and John goes there and spots ceiling panels that are out of order. Checking, he finds a photo and a case for a gun, now empty. The photo is of Turquoise, and has an address. John goes there and finds the front door unlocked. He goes in and finds he can see color pictures of the woman…in color. There is also a photo of her and John together. John goes into the kitchen and finds an elderly woman – the mysterious Yellow Teeth.
John spars with the mysterious woman over a cup of tea, and she claims she knows him "once upon a time." Yellow Teeth identifies the woman as Theresa and refers to John as "Thomas," claiming he was her favorite. She advises that he proceed slowly and when John starts to call the police, Trenchcoat Man tasers him unconscious.
John wakes up in a strange white room where Yellow Teeth torments him over the intercom with vague hints of his unremembered background. She identifies him as Thomas Crowder, son of Henry and Caroline, born Valentine's Day 1971 in Sweetwater Idaho. Then she shows him footage of his life as a farmer's son, until the day he suffered from progressive white-matter deterioration disease, and his parents took him to her organization, a consortium of unique scientists and physicians unencumbered by the dictates of regulatory agencies. John and six other children were entered into experimental treatment and three survived – Teresa of Des Moines and Michael of Baton Rouge. The marking on his chest is a scar left from removing a medical monitor device. John's color blindness, phobia, and enhanced mental abilities were side effects that of the treatment. Then John disappeared for three years until now. Yellow Teeth appears in his cell and claims some employee killed the detective. She says he's free to go and investigate, to find his peace of mind. She disappears and John finds a door that leads out into a dark alleyway.
John drives to Sweetwater, Idaho and finds the Crowder barn, where a man greets him and introduces himself as Warren Barker, who says he and his wife know about John's amnesia. Barker says he owned the property next door and that the Crowders died just after John disappeared and he takes John to their graves.
Warren and his wife Cassie bring John into their home and talk about his childhood and his love of the song "My Funny Valentine." John notices the only things he said on the Most Wanted but they admit John is understandably suspicious and show him a cookie jar he made for his mother as a child. Warren takes John to help break a horse and after a few tries John calms it down. Later Cassie reveals that John was going to marry Theresa but then John disappeared and Theresa left to find him and never returned.
John prepares to leave and Cassie gives him a plateful of homemade muffins. On the way back to Seattle, John eats one of the muffins and notices that there's a printed expiration date on the bottom. John returns to the Barkers' home…to find it empty with all furniture and identifying markings gone. The Trenchcoat Man is watching through binoculars and sends a message to his superiors – Abort!!
John returns to the alleyway where he left the facility and opens the door…only to find a parking garage. He then goes to Theresa's house where there's been a suicide attempt, and John goes into a fury. Frank and Avery show up to bail him out and he sees the woman – who isn't Theresa. The inside of the house is different – it's a mess with cats and hundreds of John Doe photos scattered around. They also find a portable electrical device that was used to kill the detective. John sees (in color) a red phoenix token which fades to black and white as he picks it up.
Avery discovers the woman was an obsessive fan who had stalked celebrities before. Avery is skeptical and John doesn't have the photo of him and Theresa from the house. Avery reveals her fiancé on the force was killed and she can sympathize with John but that her feelings endangered others as well. She recommends he take a vacation.
John contemplates the phoenix token and tries to determine if they're all tied together. Meanwhile Yellow Teeth meets with the Trenchcoat Man and they meet with a man in a stocking cap. The Stocking-Capped Man hand-signals that Yellow Teeth failed and she apologizes for not using the truth. She asks for forgiveness and her superior says nothing but merely walks off. The Trenchcoat Man kills her from behind with a small shiv marked with the Phoenix sign.