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 hugger. 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, hugging 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 himself with John's mark and didn't have any deep connection to him.
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.