A man is collecting newspaper clippings of John's exploit and watching the Most Wanted tape he made. He considers John's face, then later breaks into John's apartment while wearing night-vision goggles. He checks out John's computer files and examines everything, including John asleep in bed. He sees the brand and gently traces it without quite touching it, then takes a picture of John.
Later Frank and Stu are investigating a murder scene when Avery arrives and asks for an update on the most recent killing of a new serial killer – a female limousine driver dead less than an hour. It's the third victim of the killer and there's one clue – a piece of paper with John's brand drawn on it.
John is posing for Karen's sculpting at his apartment when Frank arrives and shows him the clues about the killer, "the Mourner," because he leaves a mortuary condolence card on each victim, with a clue to his next killing. Each card also has John's chest symbol on it. John deduces from the most recent card and its reference to 1857 Thomas St. that it's a reference to an architect in 1857 who built the Seattle sewer system and 1857 is when a gate opens. They head into the sewer and find a man suspended upside down as the sewer level starts to rise. The man has a card-symbol attached to him and they free the guy and take him to the police station. The sewer maintenance worker, Lenny Pescoe, can't help them identify the killer and can only give a vague description.
The new card talks about "Blue Light Special ATF PR" and John tries to analyze the clue. He takes off his wet shirt and Avery notices the symbols and realizes it's the same mark. She wonders if he's the killer and is not comforted by John's reassurances. John wonders if the killer is trying to get his attention, or if he put the brand on John. Stella flirts with John but they're interrupted by Frank who calls him in to help with the investigation. Pescoe is going by and comments that "Blue Light Special" refers to a strip bar and "PR" to "Pervert's Bar" the front row.
John and the police head to the strip bar and they check out the front seats and find a beneath one of the chairs. The police start to evacuate but the Mourner contacts them over the radio on a secured frequency and tells them to stop. He asks to talk to John and he spars over their "game," and tells him the bomb will release nerve gas unless John solves the rainbow. John must arrange the four strippers in the order of the rainbow, and if anyone gives him a hint he'll detonate the gas from remote, and will detonate if he doesn't solve it before the song ends. Despite being color-blind, John manages to figure out from the manufacturer symbols and their birthdates what color clothing they're wearing, and the Mourner congratulates them before leaving just as the police find the room with the security cameras that he observed the entire thing.
Back at police HQ, Pescoe returns to both thank them and take credit for solving the clue. they're interrupted by a police call from the Mourner who tells John to look under the copy machine. There's a bomb package with a brand-card on it and they evacuate the station. There's also another condolence card saying they have until sunrise and talks about "black and white." Inside the box is a jigsaw puzzle – all in white. John and the police work feverishly to solve the puzzle – John's abilities are no help with a random jigsaw pattern. Digger shows up with coffee and doughnuts and they manage to put the puzzle together but it's blank…until they expose it to black light. The clue about "Pan-Seared Pawn" leads to a Chinese restaurant with a typo where they find two policemen tied to a crate filled with explosives. The Mourner calls and talks to John, explaining his new game – the bomb is pressure-sensitive and he must pick the right cop. Removing one will disarm the bomb, disarming the other will set it off and kill them both. John has until the traffic signal turns red to solve it, and he must rescue "the right cop." John over-complicates the situation analyzing all the clues and Avery figures out it's the cop on the right and gets him off just in time. The Mourner calls back to warn that John cheated and next time he can't have any help.
John takes off on his own to contemplate the case and goes into a cathedral where Avery talks to him and advises him to have faith. John is skeptical and Avery admits she isn't a regular churchgoer recently since the death of her fiancée. She advises him to believe in what he can control, even though he thinks he can't control any of it.
Back at police HQ, Digger is serving food to the troops while they wait for the next clue and they examine the pattern of killings. John figures out from the location of the three clues that they're talking about Castle – Knight – Pawn. John identifies the particular chess game and narrows down the final move to a three-block area…which includes the police station. A policeman reveals that Stella is missing and there's a card – the Mourner has taken the "queen" and dares John to track him down.
They review the video tapes and conclude that the killer is somehow still in the building since there's no recording of him leaving the building. The clue talks about "making it to the other side" to rescue the queen. Digger steps in to point out that the Mourner isn't in the building…but below it in the sewers. Digger, a former sewer worker, manages to find a way down and John goes to check it out. He finds a chamber with Stella at the other end in a watertight chamber filling with water. There's wires laid out in a chess board and John carefully makes his way through the grid and figures out that Lenny Pescoe is the Mourner. Lenny used a pre-recorded remote device to leave the copy-machine warning earlier even when he was present. Lenny claims they're more alike than John knows and reveals he has a chest brand just like John's. He leaves John to choose rather he pursues Lenny or saves Stella then takes off. John grabs a pipe and shatters the glass container, saving Stella.
John tends to Stella and they share a moment as Stella asks again about the date, and John agrees.