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 inactive person behind. The gang bury Karen and decorate her building with her last painting.
But the mystery isn't quite over andmdash; John gets a report that 'Yellow Teeth' is barely alive andmdash; 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.
The series is about the life of John Doe, a mysterious man who rises from the primordial waters of an isolated island, possessing knowledge of literally everything in the world, yet having no memory of who andmdash; or even what andmdash; he is. Doe quickly finds his way to Seattle, where he befriends the police and uses his special gift to help them solve 'impossible' crimes each week, while continuing his unending quest to uncover who he is and where he came from. Despite his considerable charm, Doe is an emotional island unto himself. Want to know the population of Peru in 1853? How many blue cars there are in the state of Washington? Or better yet, predict which horse will win every race at the track based on knowing all the variables? Doe has all the answers. But what is he like? Family man or loner? Hero or villain? What is truly in his soul? Doe doesn't have a clue. In his search to unlock the key to his past, He may be a government agent, an extra-terrestrial or perhaps just a regular guy.