A man awakens on an island only to discover that he has no memory of who he is. Without knowing his identity, he travels to Seattle and finds out that not only is he an amnesiac but that he is a savant, that he knows literally everything. The colorblind genius soon becomes a police consultant, aiding in the most inexplicable of crimes, while, at the same time, beginning a journey to find out who he is.
Karen is fired from her job at the bar by Digger. She talks John into taking her on as his assistant. Also, John helps the Seattle Police figure out the motive behind a series of attacks against an importers family.
A woman shows up with a young boy, and claims this is his son. She was part of a project that John may have participated in. Several geniuses donated genetic material, any one of them including John may be the boy's father. Someone is killing the donors, the race is on to find the killer and the boy's father.
John Does decides to go on a trip to London. He's struggling to calm himself down due to the claustrophobia caused by being on a plane when a Reverend dies. John finds out he was murdered (poisoned).He has to find the killer, who is on the plane, with a help of some people and others trying to make his job harder.
Rachel visits John in Seattle. New to relationships and dating, John seeks out advice from Frank. A popular deejay dies under peculiar circumstances. John and Rachel work with the police to figure out how it happened.
It's all about families. Frank's soon to be ex-wife wants sole custody of their children and she wants to prevent him from seeing them at all. A teenage girl is kidnapped by a deranged man who wants to replace his family.
The Phoenix group kidnaps Karen to interrogate her about John and an artifact that they seek. John follows a trail of clues and a series of deaths that lead him back to Horseshoe Island. Will John and the police find Karen in time to save her?
An astronaut who falls from the sky is shot by teen aged campers. The autopsy reveals that the astronaut would have died of asphyxiation if he wasn't shot. John, Frank, and Digger investigate the mysterious burned-out circle found near the shooting.
After being struck by lightning, everything changes for John Doe. He can see colors, but he no longer has his super intelligence. He makes financial mistakes. He is not as effective for the police. All of this makes him doubt himself.
The Seneca Institute has an interesting program involving "fallen geniuses", psychic abilities, and remote visions. John Doe and Digger stubble onto it while investigating an accident to Digger's blood brother.
John is having visions that cause him to black out. The visions lead him to the dead body of an unidentified man. Several clues on the body of the unidentified man lead Doe to the Phoenix Group. What he learns is mind blowing.