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 killer. 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, killing 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.

Ken Rothman, an ex-police officer that Avery got fired for beating a suspect, gets into the police HQ by faking his death 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.