At a mission house, several people are looking up at the approaching lightning storm. At The Sea, John is playing a game of "Stump John Doe" Digger collects the pot while John notes that he'd like to be stumped just once. At the mission, a man walks off down the alleyway when a figure in a poncho comes at him with a knife. He turns to run but the figure appears behind him and kills him.
John is walking home when lightning starts coming down around him. He runs but is hit in the chest by a bolt and he goes down, unconscious.
Paramedics and Digger wake up John and tell him he's okay, even though his shoes were burned through and he has numerous burns. John refuses to go to the ER and heads home. The next morning, Frank and Avery are checking out the corpse while John wakes up and starts getting flashes of color. Frank calls him in and they identify the victim as a Thomas Sullivan with one prior. Nance determines the killer bled him out and then kept going, removing one of his kidneys. John is upset by the sight of (colored) blood and takes off. But he quickly realizes he's lost his reflexes for driving.
At his apartment John takes time to admire one of his paintings and then his broker arrives to find out how John wants to handle his investments. John is puzzled and then heads to the bar where he can't answer a question about a drink recipe. John finally admits that he doesn't know…anything. Digger suggests he relax and take a break and John starts to embrace his new life. But when he arrives home he finds a package and a letter signed "JTR" expressing admiration for him and hoping to meet him at midnight. Inside the box is the missing kidney.
John takes the kidney to the police morgue and John (badly) bluffs his way through knowing something useful. He's reluctant to admit he's of no use to them and directs them to Stella. She comes up with a lead on the paper and they come up with a purchaser with the initials JTR and John fakes confirming it. A woman, Samantha Sullivan, comes in and introduces herself to John as the dead man's sister, and he wasn't someone who normally hung out near the mission. She basically guilts John by saying she's counting on him to solve the case. Avery and Frank reveal the JTR they brought in couldn't have been the killer. When Avery tells him to take a break, John takes it hard and leaves.
That night John smashes a mirror in frustration. Digger shows up and John questions him about whether he's Digger's friend because of his smarts. Digger says it's a matter of loyalty and John admits he's feeling useless. Digger suggests they might be able to reverse it and John reveals the brand is metal and it drew the lightning. It's fifteen minutes to midnight and John goes through the phone book, but Digger realizes the initials stand for Jack The Ripper. Out in the streets, the killer stalks another man, corners him, and kills him.
The next morning they determine two men were killed at approximately the same time. Avery and Frank are puzzled but reluctant to call in John. At the library, John tries to look up info on Jack the Ripper but is recognized and can't answer any questions. He flees in frustration back to The Sea, where his broker tells him that the cattle futures John told him to hold on went belly-up and John is broke. Digger offers him a job as piano player again but John can no longer play piano either. John has no choice but to sell his car.
Frank tells Avery that John has connected the killer to Jack the Ripper, and the killer is following the same pattern of killings. The killer is fixated on John just as the original Jack the Ripper sent clues to an investigator helping the police in the 19th century. Avery goes to John and figure out he's doing research, and John admits all of his knowledge is gone. A bitter John accuses Avery of just using him to solve mysteries and she stalks out.
Later John is drinking and unable to solve a crossword puzzle. He staggers out into the streets and yells out to "Jack," then returns home to find a message in blood saying that he's next.
John is back at The Sea and in protective custody, with Avery and Frank watching over him. A woman comes in and complains that her friend abandoned her and she needs to walk to her car. John offers to help her and they go out, but then the woman takes offense at something he says. Then they hear a woman scream and go to investigate. John finds a woman lying in an alleyway but it's a bundle of rags. The killer comes at him from out of the shadows and hits him, and it turns out the "killer" is in fact two women. One of the sisters was a prostitute disfigured by her john. They come at John and slice open his shirt, revealing that he's wired and it's a trap.
The sisters flee and John pursues one of them up a fire escape. The police arrive and take one sister while John's kicks him off the fire escape and into an electrical light. John wakes and realizes he's back to "normal." John had figured the killers were women and planned the whole thing, and more then happy to start rattling off facts and figures.
John is back playing at the piano when Avery comes by to drop off a statement. She assures him there's no hard feelings about his earlier insinuations. They share a brief moment before Frank arrives to set up another round of "Stump John Doe." He starts him with a few questions and then stumps him by asking John the color of his shirt.