As he tries to figure out his own identity, an amnesiac genius with an encyclopedic knowledge of apparently everything helps Seattle police solve mysterious cases.
John tries regression therapy in an attempt to both solve a gruesome murder and unlock the secrets to his own mysterious past.
A stranger identifies Doe as the chief suspect in a murder that took place decades ago.
John finds that a man whose circumstances mirror his own may hold a key to his identity.
John is shocked to see that Karen is the prime suspect in a murder at a museum.
John may have a clue to his identity when a woman and son approach him claiming that based on records from a sperm bank, John is the father. Also, strange murders occur where the victims' brains are removed.
Following the clues to the death of a PI that was following him, John arrives at the feet of Yellow Teeth. She provides him with his life story, but he doubts the honesty of the source.
John happens upon a flight where passengers and crew members are die mysteriously.
John contends with a serial killer who goes by the name of the Mourner who just happens to know a surprising amount of information about John.
In a personal case, John Doe must solve the crime behind Lt. Avery's abduction. The big clue left at the scene: a piece of paper with a symbol identical to the identifying mark on John.
John Doe juggles a club DJ's inexplicable murder and the possible appearance of love in his life.
John tries to stop a criminal who is reassembling his dead family with various victims.
A mysterious group kidnap Karen, hoping for information about a Phoenix staff, and John may not be able to reach her in time to save her.
John tries to cope with Karen's death and his guilt over not being able to save her. In the meantime, he lets a psychic help him solve some murders taking place in a park.
John tries to get through a government cover-up to solve the odd death of an astronaut.
John Doe is caught in a hostage situation and quickly becomes one man fighting against the terrorist threat.
John tries to help an internet-based escort regain stolen property only to find it has ties to human brain research and the Phoenix organization.
John must solve a case as a layman when a bolt of lightning robs him of his accelerated intellect and talents.
The death of a former military friend of Digger sets John on the trail of his mystery that reveals experiments in "remote viewing," seeing things from a great distance away.
John Doe enlists help to control the visions that begin to assail him and uses that help to track down the Phoenix organization and their captives. Doe rescues Teresa, the girl he's been after, and the face of Stocking Cap is revealed.