At The Sea, John arrives and wonders about the woman who called him "Tommy," and analyzes the piece of window from the ferry. As Digger and Karen look on, John relates how he lost the woman and then obtains a fingerprint from the glass.
A man, Pickford, steps out of his house and dives into his pool…which is filled with blood. Hayes shows up to investigate but the lab isn't hopeful they'll find anything. The security systems are undisturbed and there's no trace of blood in the pipes – Frank is puzzled and reports back to Avery, and all the lab can conclude is that it's from a recently deceased individual. John shows up to have Frank check the fingerprint, and Frank mentions he's checked into John's background and noticed he's reported himself missing, before agreeing in return for John helping out with his case.
They go to the Pickford pool and John notices the Pickfords' daughter, Shayne. They talk briefly but she isn't helpful. After she leaves, John climbs up on the roof and figures out someone ran a hose through the drain pipe and into the pool. John spots a footprint and concludes the person was 130-140 pounds, probably a woman, and then finds a petal which he tracks down to a valley where Pickford has a brother. They head out there and check out the barn, where they find Pickford's brother dead, drained of blood.
John concludes Pickford's brother was professionally embalmed, and Avery shows up to gripe about John's involvement. John figures the victim was alive when he was exsanguinated by the killer. Later John heads out and while putting up posters he notices a jewelry store with wedding rings and wonders if the woman he saw is his wife. He picks out a ring to try on, but can't get it off and buys it. Later at The Sea, John is playing when Avery comes in and when they verbally spar, John still tries to offer his help while Avery is suspicious of him and his lack of background. Later, Karen shows up at John's apartment and he's still obsessed with the mystery woman, redecorating his apartment to suit the woman's imagined tastes. Karen is freaked out by his obsession and then Hayes arrives and Karen, an artist, acts for their opinion on her paintings.
After she leaves, Frank reveals he has no match on the fingerprint. He does reveal that the autopsy confirmed John's theory but they've found nothing. The victim was cleaned after death but there's traces of a rare herb – John concludes the herb relates to a Buddhist ritual used to prepare the deaf for the afterlife, and Pickford did business in Vietnam. They track down the four funeral parlors in Little Saigon and John finds out about a missing embalmer, Nguyen. They go to Nguyen's apartment and find evidence confirming he was involved. The man comes in, spots them, and flees through the streets, losing them after a brief chase.
Later Frank and John check the security camera of ATMs that Nguyen ran by and track him to the docks, then head for the dock owned by Pickford's company. At the office, Shayne clocks in, unaware she's set off a hidden fuse. Mr. Pickford arrives and the place bursts into flame – Pickford tries to put out the fire with an extinguisher but John arrives and stops him. John spotted that the fire extinguisher was the wrong type and a test determines it was filled with phosgene gas. Avery takes Pickford into protective custody while the mother and daughter are sent off to visit Mrs. Pickford's mother. Avery thanks John for helping out, sort of, and then he talks with Shayne, showing him his brand-mark. Shayne starts to talk about her screwed up family but has to leave with her dad, but not before suggesting his brand might be an astrological mark.
John returns to his apartment to find a clearly upset Karen waiting for him – she's been fired for being underage, but she wants to help out as John's assistant. John isn't too enthused about the idea but Karen points out he's looking for company no matter what he says about being a loner. Later at The Sea, John and Digger commiserate over marriage, and then John goes back to the Pickford case. He discovers that one shipping crate is missing from Pickford's inventory and they figure it's in the water. They bring it up and it contains a number of corpses.
Back at Nguyen's apartment, they've concluded the Pickford brothers are smuggling illegal aliens and dumped the immigrants, killing them. They conclude Nguyen is gong for revenge and John spots some photos that show Nguyen knows where the safehouse is where Pickford is located. The police take off while John studies the picture of Nguyen with his daughter, and figures he'll go after Shayne. He heads there, "borrowing" a motorcycle to get through traffic. Nguyen is preparing to shoot Shayne with a poisoned dart gun but John gets there just in time to try and talk him out of it. Nguyen doesn't buy it and John manages to knock him down, where he shoots himself with the poison dart and kills himself.
At police HQ, Avery concedes that maybe John can help her out from time to time. John talks with Shayne and assures her she'll be okay. At the ferry, John talks with the hot dog vendor again, who assures him whoever he's looking for will turn up when he's not looking. As he walks away the wedding ring comes loose and he decides to throw it away…and stop looking. At The Sea, John changes his mind and tells Karen he can use her as an assistant. He also notices a newspaper article on his police assistance, and hangs it up on his wall. He's unaware that in a secret office somewhere in the Middle East, a woman with yellow teeth receives a copy of the same article, and it's clearly she knows something about John Doe.