Ken Rothman, an ex-police officer that Avery got fired for beating a suspect, gets into the police HQ by faking his passing and he and his men quickly take the station and most of the staff (except Frank) hostage. Rothman demands his reputation be cleared, but John manages to get free and escape into the building, and soon discovers Rothman has a supply of Russian-made smallpox. John manages to take out a few terrorists before being recaptured and Rothman leaves John and Avery behind with a shattered vial of smallpox. It's fake, but the whole thing is a ploy to get hold of smallpox vaccine to sell as a bio-weapon. Doe figures it out and they capture Rothman just in time.
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.