Season One | Episode Guide

Pilot
Doe awakens to find himself stranded on an island off Seattle. His uncanny newfound abilities are soon apparent to him, however, when he is rescued by Asian fishermen and begins to speak the sailors' language fluently. Later, as he watches a news report about a kidnapped girl, the color-blind Doe realizes that he is seeing the child in color. Sure that she holds the key to the mystery of who he is, Doe is eager to find her and offers his assistance to the skeptical cop who's working the case.

Blood Lines
While continuing his quest to figure out who he is and from where he came, John Doe must use all his unique abilities to solve a gruesome murder case, initiated when a seemingly innocent individual dives into a swimming pool which he discovers is filled with human blood. Meanwhile, Lt. Jamie Avery, impressed with Doe's ability to help the police with the case, attempts to surreptitiously learn his real identity. Karen is fired from her waitress job at The Sea and convinces Doe that he needs her as his assistant. Also, a mysterious woman may have information on Doe's identity.

Do Re: Me
Victims turn up cut in half and the police call in John. DNA leads to a suspect locked up in an asylum who claims he can leave the place in dreams. John tracks the man's twin brother, actually a transsexual, and after another victim turns up he concludes that the twins were separated at birth and the victims are the child-service officials who had them separated and their mother is the one taking revenge.

Meanwhile, after hypno-regression therapy fails, John tries dating which doesn't go over well. After a brief sensory-deprivation session with the asylum doctor, Jansen, John has some vague visions but Jansen disappears along with the session tape. The police believe the same killer disposed of Jansen, but we find out he's been killed by the mysterious woman we saw at the end of the previous episode.

Past Imperfect
When skeletal remains are found at a construction site, ownership of the property is traced to a man named Stephen Prescott about whom little is known except that he bought the land in 1960---and that he happens to be a dead ringer for Doe. More disconcerting is a visit to the murder victim's widow. She hasn't spoken in five years, but when she sees Doe she spits out one word: "murderer."

Shaken, Doe is convinced by Karen that he might be a time traveller and agrees to test a professor's theory that such travellers would have to be given amnesia to avoid time paradoxes and submits to an MRI. But in the aftermath of the test, he begins experiencing lapses in time, flashes of color-vision, and odd visions. The victim was the Prescott's maid, who provides a picture suspecting John may be Prescott's son and thus the family resemblence. But after the next blackout he wakes up with the maid's corpse. The police eventually track down Prescott who's hospitalized but Doe eventually sees through the deception and they intercept the escaping man who crashes and his body can't be identified. John's memory blackouts seem to be over and all he has is more questions.


John Deux
Doe suspects a link to his own identity when a naked man with a similar brand and no recollection of who he is washes ashore from Horseshoe Island, similar to Doe's arrival in town. But then the mystery man disappears from the hospital and the trail leads to a mysterious doctor who offers to knock John out and take him to the answers. John escapes long enough to send a signal to the police before the doctor, a black organ surgeon named Dorman, can remove his heart. The police arrive and save John, the police track down the mystery man (who was also killed by Dorman), and the doctor kills himself before revealing anything about what he knows of John.

Low Art
Investigating a violent and seemingly impossible crime committed at the Seattle Museum of Art, John quickly deciphers the method but a security camera shows his assistant Karen escaping out a side door. John quickly clears her of involvement by acting as her defense attorney but Karen is connected to the main suspect, photographer Max Clark. He has an alibi to and Karen leaves at John's apparent betrayal. The body of the museum guard vanishes and John connects it to Clark who slipped in and stole the body with the diamond inside. It turns out the dead guard was dying of cancer but the museum denied her insurance, so she set up the heist, swallowed the diamond, and cut a deal with Clark so her son would get the diamond. Clark ends up going to jail anyway, while John and Karen resolve their issues.


Mind Games
When a young boy Wesley and his mother approach John Doe claiming that sperm bank records indicate he is the boy's father, John is pulled into a mystery as he tries to track down the list of donors and finds two of them dead, their brains removed. He meets the others who are also geniuses while bringing Wesley along. that will not only force him to perhaps come face to face with his past but also explore emotional and personal connections that have been absent from his life. John races against time to stop any further killings and protect wesley. It turns out the murderer is one of the donors who believed the project was twisted and evil. John and Frank track down the killer to the fertility clinic before he can kill Wesley, and they discover that John isn't the father. At the end, the mysterious "Yellow Teeth" looks over photos of John and says "It's time...


Idaho
The murder of a private detective by a deaf killer (the Trenchcoat Man) leads John to the house of the woman on the ferry, Teresa, and a confrontation with the enigmatic woman with the yellow teeth, who addresses John as "Thomas Crowder" and is in league with the killer. They capture John and the woman reveals his supposed background. John was a farmer's son from Idaho suffering from a fatal brain disease and her organization stepped in to provide a cure to John and two other children as part of "The Program." The side effects resulted in John's amnesia, gifts, and quirks. The woman on the ferry, Teresa, is one of the other two children.

John is released and told to investigate so he travels to Idaho where he supposedly grew up. He meets the Barkers, his parents' neighbor who recognize John as Tommy and reveal his parents are dead. He bonds with them and fill in some gaps in his memories. But John figures out they're fakes and when he returns everything is abandoned. When he returns to the house supposedly belonging to Teresa he finds a suicide but doesn't recognize the woman. The house is covered with pictures of John and the evidence makes it look like the woman was a stalker who killed the detective. John is left with a strange phoenix token and clues that go nowhere. Yellow Teeth meets with another deaf individual who chastises her for lying to John and then has her killed by the Trenchcoat Man . . .with a knife with a phoenix pattern on it.


Manifest Destiny
Doe boards a flight for London but his vacation gets off to a rocky start when a murder-mystery unravels in midair. A claustrophobic Doe takes his mind off his troubles by getting to know a pretty fellow passenger, Rachel Penbroke, who also happens to be a neurologist. A minister screams his way into first class and promptly falls dead. Doe's diagnosis of murder is confirmed when Rachel identifies traces of strychnine poison on the dead man. Things rapidly grow worse when the co-pilot is killed with a ballpoint pen while the pilot passes out from carbon dioxide poisoning. John is forced to pilot the plane when they hit rocky weather and barely manages to stabilize it until autopilot takes over.

John soon discovers that the minister was an unintended target because he was assigned to the seat at the last minute. John figures out the intended victim is Rachel but he panics and the passengers lock him up. John manages to get hold of the weight-lifting team he befriended earlier. John rigs a gas to detect blood traces and one passenger goes missing – the one who takes Rachel down into the hold and depressurizes the area to get revenge for his mother, whom Rachel rejected from her program. John manages to get the drop on him.


The Mourner
The mysterious symbol on Doe's chest is part of the calling card left by a serial killer known as The Mourner who knows a lot about Doe, whom he challenges with cryptic clues as he puts more lives in danger. John manages to rescue a sewer worker, Lenny Peska, but the killer designs a series of killing-traps keyed to John's weakness: color-blindness, tendency to overthink things, and the like. John finally figures the Mourner is using the city as a chessboard but the killer responds by snatching Stella. With Digger's help John tracks the Mourner to the sewers where it turns out he is Peska, who has a similar mark to John's and taunts him with hints he knows more about John than John does. John is forced to choose Stella over the escaping killer.


John D.O.A
Lenny renews his duel of wits with John, kidnapping Lt. Avery and sending a series of cryptic clues with a fatal deadline. A new captain makes things hard for John and he and Digger go off on their own to hunt down the killer. John meets up with Frank and they figure both that the police are on the wrong trail going into a booby trap and where Lenny really is. But Frank accidentally shoots John, killing him and letting Lenny escape. It's a ruse to draw Lenny out at the cemetery with no one in the way, one that (more or less) works. We do find out that Lenny branded him with John's mark and didn't have any deep connection to him.


Tone Dead
Juggling his personal and professional lives like never before, John Doe finds himself pulled in different directions when a murder case beckons his abilities just as a potential love interest shows up on his doorstep. When a young Seattle DJ is mysteriously murdered by a seemingly non-existent perpetrator, Doe helps unravel the enigma while pursuing a relationship with Rachel Pembroke. As smitten with her as he is, Doe is tormented by the thought that he may have a significant somebody in his life already that he does not remember, and must decide whether to live in his past or present world.


Family Man
The case of a mysteriously kidnapped teenage girl sends John Doe and Det. Frank Hayes on a frantic investigation to save her before it is too late. When clues lead them to what they believe to be the remains of the girl and others, they start to piece together the evidence and discover the gruesome notion that a psychotic suspect is trying to replace, piece by piece with unsuspecting victims, the family he has tragically lost. While working together on the case, John develops a better understanding of Hayes' family situation and reaches out to him in a touching show of friendship.

Ashes to Ashes
Returning from Karen's art show, John thwarts a bomb threat but it's a ruse for the mysterious group that's been plaguing John to grab Karen. The group thinks John knows something about a staff with a phoenix on it and Karen may know it as well. The trail leads to a warehouse full of dead deaf people and then John gets snatched by the NSA. They want to know about "Phoenix" but John doesn't have a clue and the head guy, Sam, lets him go eventually. Karen manages to call John long enough to give him a clue leading him to . . . Horseshoe Island. Phoenix has evacuated it after an extensive excavating operation, leaving Karen's corpse behind. The gang bury Karen and decorate her building with her last painting.

But the mystery isn't quite over --- John gets a report that "Yellow Teeth" is barely alive --- he visits her and she warns that Phoenix is seeking a staff tied into his destiny and they won't stop coming until they get it. She dies, and the audience sees the staff is in the Vatican.

Psychic Connection
John copes with his first nightmare over Karen's death while helping the police in the deaths of several young girls. A psychic, Delphine, helps them locate two of the bodies in a nearby park. John is skeptical of her abilities but begins to believe she has some gift when she sees a presence and a darkness about him. After the third girl turns up dead, Delphine leads them back to the park where they find a skeleton from five years earlier . . . around the time she started blacking out and her gift started manifesting. John determines that Delphine survived the killer's attack and suffered amnesia, thus explaining her "psychic" connection to the killings and the park. John soon determines all the victims worked in food services, and that a butcher, Jeb Crosby, is the killer . . .but not before he captures Delphine. John and the police arrive just in time to save her and John comes to terms with his guilt over Karen's death.

Illegal Alien
High school kids are surprised by a bright light in the forest and an astronaut who walks toward them that they shoot. The police and John investigate and determine the astronaut actually died of cyanosis but a Colonel Dunagan moves in and take the body -- John taps into satellite photography and sees a blast pattern that matches the one on Horseshoe Island that accompanied his arrival. John, Digger, and Frank sneak into the woods to examine the site and find a large pod. The pod is a Mars environmental test system and inside the trashed interior are a bunch of astronauts dead just like the first astronaut --then they get sealed in. Meanwhile Avery pursues her own investigation despite the military government and after interviewing Dunagan's staff sergeant, believes Dunagan is involved. The men start sniping at each other due to cyanosis symptoms while Stella and Avery track them down. John uses its navigation beacon to send out a SOS. The Staff Sergeant is the one responsible, making it look like the recyclers failed on their own so a new company would win the multi-million dollar contract. Fortunately, John manages to fix the recyclers in time and they capture the Sergeant when he shows up.

Doe or Die
Ken Rothman, an ex-police officer that Avery got fired for beating a suspect, gets into the police HQ by faking his death and he and his men quickly take the station and most of the staff (except Frank) hostage. Rothman demands his reputation be clear, but John manages to get free and escape into the building, and soon discovers Rothman has a supply of Russian-made smallpox. John manages to take out a few terrorists before being recaptured and Rothman leaves John and Avery behind with a shattered vial of smallpox. It's fake, but the whole thing is a ploy to get hold of smallpox vaccine to sell as a bio-weapon. Doe figures it out and they capture Rothman just in time.

Save As... John Doe
A woman, Paulette, picks up a locked case and has it stolen, then comes to John for help. Moretti, a dead scientist, developed chips to augment the human brain and left them to her. John accepts, believing chip-augmented brain processes may be connected to him. The trail leads to Moretti's house and a dead man -- the thief, then to a on-line escort service where it turns out Paulette works. John figures out Paulette has the key on her charm bracelet and opens the case -- it has a motherboard set up like a map of the city, and John and Paulette track the location to an abandoned basement being used as a lab with comatose accident victims being used as subjects in the chip experiments. Then they figure out the case contents have bar codes but when John scans them for info a hacker starts blowing up city sites through the electrical and water system and demands the case be given to him. John takes the case and tracks the hacker back to a nearby mall -- it's Moretti's assistant Johansen, a religious type who feels the chip-enhancement is a blasphemy. The lab guys disappear and John breaks the bar code system, giving them a message from Moretti who has encoded his consciousness until the lab types could transplant it into a braindead body. John turns Moretti's chip over to Paulette, while we discover that the Phoenix organization is working with the lab people.

Shock to the System
John is hit by lightning on his chest-brand and can see in color -- going to see a fresh body, John realizes he's also lost access to his vast supply of knowledge and all the physical talents it provided. It's not a good time as the killer leaves him a kidney from the body taunting him with the promise of more to come. The killer strikes again with two killings as John tries to come to terms with his newfound ignorance and the loss of his money when he can't call the shots for his broker. John is bitter and reluctant to admit his newfound loss to anyone, and a disappointed killer threatens to come after him. It turns out that two women, sisters, are working as the killers and lure John into a trap – fortunately John figured the killer(s) were women and he'd be targeted and the police have him wired and are watching. While pursuing one of the killers John is hit with electricity again and is back to being color-blind and super-smart.

Remote Control
A man escapes from the Seneca Institute and is run over -- Digger recognizes him as his blood brother Jay Dougan and John can see Dougan's picture in color. The two of them travel to Northam where the color leaves the dead man as John watches and the body has teeth with no enamel and a tag-id on his tongue. The two of them find the man's Army medal in the woods and follow it back to the Institute where mental patients are kept, but there's no evidence Dugan was ever there. They sneak in and John witnesses patients being drugged to act as "remote viewers," seeing things psionically from a distance.

John sees one blind patient, Michael, in color and playing "My Funny Valentine" and gets him out -- he has scrambled senses and says he was told he was suffering from a fatal brain disease (similar to John's history -- see "The Mourner.") and they took him in and help him develop his gift to see at a distance along with other orphans and homeless people. They realize they're being watched by Sam of the NSA ("Ashes to Ashes"), who says the remote viewing program was created by Stefano Moretti ("Save as…John Doe") and someone took the program over when the NSA discontinued it. Michael gets grabbed and taken back to the Institute, which is set on fire by its owners to cover their tracks – John and Digger get the other patients out but lose Michael. Supposedly terrorists were paying the Institute to find missing nuclear waste and Digger buries his friend and promises to stand by John no matter what. But we see that Phoenix has the viewers and are putting them to use against John.

The Rising
John begins to experience an onslaught of bizarre visions and images, which eventually bring him closer to the mysterious Phoenix organization pursuing Doe and the people connected to his past. The capture of a top Phoenix operative known as Trenchcoat leads to surprising revelations.