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John begins to experience an onslaught of bizarre visions and images then blacks out – the visions lead him to a faceless murder victim and a cannery where the Phoenix Organization and the remote viewers were situated.
The death of Digger's blood brother and fellow Special Services soldier leads John to the mysterious Seneca Institute and a mysterious project to train psychics.
John is hit by lightning on his chest-brand and can see in color. He also realizes he's lost his extraordinary knowledge...just when the police need him to solve a series of crimes based on those of Jack the Ripper.
A woman, Paulette, picks up a locked case and has it stolen, then comes to John for help. John becomes embroiled in the hunt for the case, which may hold the secret to the immortality of the human mind.
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. Only John can stop him before Rothman carries out his true plan.
High school kids are surprised by a bright light in the forest and an astronaut who walks toward them that they shoot. The crash pattern matches that of the circle John appeared in upon awakening, and he resolves to figure out what's going on.
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.
The Phoenix group continues its deadly game with John, setting a trap for him as a lure to kidnap Karen and interrogate her about what she knows John and a mysterious "staff." John must follow a trail strewn with death to find Karen before it's too late for her as well.
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 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 (from "Manifest Destiny").
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.
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 boards a flight for London but discovers a murder-mystery in mid-air while getting to know a pretty fellow passenger and neurologist.
John discovers clues that lead to his real life, a trail that takes him to Idaho and raises more questions than answers.
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.
Investigating a violent and seemingly impossible crime committed at the Washington Art Museum, John discovers that Karen is involved.
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.
When skeletal remains are found at a construction site, the ownership is traced to a man who is a dead ringer for John.
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. 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 that may hold the secret to John's past.
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. Karen is fired from her waitress job at The Sea and tries to convince Doe that he needs her as his assistant. Also, a mysterious woman may have information on Doe's identity.
In the opener, 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.
An early version of the first episode, with some script changes and with Meat Loaf as Digger and Azura Skye as Karen.
