Lt. Avery arrives home and works on her supper while talking to her pet turtle. She prepares for her shower when Lenny – "The Mourner" pops out of the shower cubicle and gases her unconscious. He leaves, laying a condolence card on the floor and wearing a bag over his shoe with a fake footprint.
Stella checks in with Frank to get an update on Avery's disappearance – the police are on it and John is checking out the crime scene. Captain Ruiz arrives to take command Frank brings him up to speed on Lenny's history. Ruiz is skeptical of Doe and Stu interrupts to show they've found a footprint. Frank is suspicious since Lenny has never left such a blatant clue before, but they run it down. John arrives and Frank warns him about Ruiz. They go over the condolence card with a picture of Lenny's shadow. John figures out the time the picture was taken from the length of the shadow and concludes they have to do something in the next twelve hours, by 9 a.m. Frank tells him a bit about Avery from when he first met her and her father.
In his secret lair, Lenny and Avery spar verbally while the lieutenant works to get loose. She gets free and goes for her gun, but Lenny has anticipated her and unloaded the gun. He uses a knife to force her back to her seat and reties her. Lenny draws blood with his knife.
Ruiz questions John about the fact they have a similar brand and is skeptical of his abilities. Avery claims John isn't interested in her but Lenny has footage of her and John talking about her dead fiancée at the cathedral. Lenny assures her that John will come for her, then activates the explosives beneath her chair. Ruiz has John taken into custody because he didn't reveal his brand, and Frank talks to him. Frank is upset John didn't' reveal the brand to him, and then he and Ruiz take off with John still in custody. John uses a pen to unscrew the light switch and then cause a short circuit to take out the lights and draw the police into the room. He leaves a panel open and then when they think he's gone through the ceiling, he takes off through the door and out, wearing Ruiz's jacket.
John meets with Digger at The Sea who offers her help, and together they plan to retrace Lenny's steps. After Digger leaves, Lenny confronts John and shows him the remote on Avery's explosives. John is forced to let him leave.
The police analyze the footprint but Frank still thinks it's a fake clue planted by Lenny. Ruiz thinks Frank is too close and then admits he knew Avery's father and doesn't plan to lose her. They get a trace on Ruiz's cell phone from the jacket Johns stole and the police close in on the transmission, only to find it's a couple from police HQ that John slipped the phone on to.
John and Digger go into the sewers to where Stella was held. They check out the crime scene and John finds a closed-system rebreather. Inside John finds a condolence card with a photo of someone wearing a sheet like a ghost. Lenny is watching them on closed-circuit camera and is pleased that John is catching on – he's eager for a real challenge. Then he goes through Avery's personal photos and torments her with the dead people in her past.
John sneaks into his apartment where Frank is waiting for him in his secret research room and offers his help. Stella has located the custom shoes and the person who purchased them and Ruiz goes after him. Frank gets the address but they're sure it's a fake clue. John runs a sample of Lenny's saliva from the rebreather mouthpiece but there's no genetic material at all. John concludes Lenny has an auto-immune syndrome that prevents the creation of saliva and tears. John tracks down medicines for the syndrome and finds a patient with the same name as the patron saint of chess. Frank warns Frank the warehouse address is a trap and the place explodes as his SWAT team break in.
With fifteen minutes left, Frank and John go to the patient's address and John confronts Lenny, who has a knife to Avery's throat. Lenny taunts him to outsmart him and John drops the gun, but Lenny realizes Frank is closing in. Frank barges in and Lenny accuses John of cheating, John jumps for Lenny and Frank takes the shot, killing John.
At John's funeral, Digger says a eulogy over the casket and they depart. That night Lenny digs up the casket and opens it, confident that it's a fake. He finds John inside, dead. Lenny loses it, upset his one challenge is gone and that nobody can stop him now. Frank announces himself – he, Ruiz, and the police are there to take him into custody. Then John climbs out of the grave behind him. John reveals he was wearing a Kevlar vest, used Lenny's rebreather in the coffin, and overcame his claustrophobia to lure Lenny in. Lenny maces a policeman and uses him as a shield to get into a sewer tunnel. But when he gets underground Avery appears and puts a gun to his head, taking him prisoner.
At Digger's bar, everyone celebrates and Avery shows up to berate John…just as she once berated Frank for saving her by shooting a suspect. John thanks her and Avery reveals Lenny's brand was self-inflicted – he has no real connection to John. They invite Avery to join them for a game of darts and she reluctantly accepts…and starts kicking their butts.