At a bank, a woman named Paulette Chambers goes through identification protocol and collects a briefcase. She wonders where the key is but there isn't one and she has no idea how to open it. She and her dog leave but down in the parking garage a man grabs her and throws her aside, then takes her van and leaves with the briefcase and the dog.
At The Sea, John is bored and somewhat depressed that Rachel has moved back to London. He's interrupted when Chambers enters, asks him if he's John Doe, then collapses.
When she recovers, Paulette asks John for help and reveals the case belonged to a crippled software billionaire, Stefano Moretti, who focused on artificial intelligence and believed humans could have enhanced intelligence through implanted chips. Paulette reveals she was his personal assistant and asserts it must have been valuable. She believes the case has "The Answer" – a way to link humans to computer intelligence. John agrees to find her van by morning, and Paulette clearly is putting the moves on him.
John ties into a satellite to look for the dog's electronic collar and narrows it down to an address – Moretti's. Moretti's house was automated and John and Digger go there and find the van with the dead dog. The house "senses" them and recognizes Digger from the criminal database. The lighting starts to short out and as they look around they spot the thief, dead.
Stu determines the thief was electrocuted when touching the door handle. The security system was designed to stun intruders but the thief got triple the charge. Stella taps into the security cameras and sees the thief came to the house with the case. John starts to explain when Moretti's assistant shows up…and it's not Paulette. The assistant, Randall Johansen, explains that Moretti's system would let someone download their intelligence into computers. Johansen has an iron-clad alibi and leaves. Digger displays enough knowledge to get into the computer system and determines how the intruder bypassed the system. There's a mention of "Xanadu" and a web site, Kubla.Com.
Frank and John go there and find the place is an on-line prostitution set-up. John spots Paulette and they bring her in where Avery interrogates her. Paulette recognizes the thief but denies having anything to do with the murder. She does admit she was a "virtual companion" for Moretti and could interact with the house by remote. Avery lets her go and John figures she's using him. John goes back to Kubla.Com and checks out Paulette's dressing room, where she confronts him. She flirts with him some more but they're interrupted when a man barges in with the case and demands the key for the case. He tries to escape when another thug with kung fu skills hits him and the guy drop the case and runs. John fights the kung fu thief and drives him off, recovering the case.
John figures Moretti designed the case so only Paulette could open it, and spots a necklace she's wearing. He uses the key to open the case but all it holds is some papers, common items, and a motherboard laid out as a city map for Seattle. They pinpoint a building where Moretti met Paulette and go there to find a secret laboratory where four people are held in suspended animation.
Frank comes in and talks to the head doctors, who reveals they're legal and using comatose accident victims for an experiment on behalf of Moretti. The head scientist tells them to leave and Frank plans to return with a warrant. They talk to Johansen who knows nothing about the lab, and Avery identifies the electrocuted thief as a drug runner – Johansen doesn't recognize him. After he leaves, Frank reveals Moretti and Johansen weren't on good terms, and Paulette picked up computer skills recently. John and Paulette have a moment and Paulette asks him to stay. They chat and finally share a kiss but before it goes further, John spots a bottle of perfume with a Universal Product code and takes off.
John meets with Frank and Stella and reveals that Moretti used the items in the case and their bar codes (with extra numbers) to store his info. Before they can go further they get an outside e-mail and a link to the Department of Power & Water. The person at the other end identifies him as The Lord Thy God and demands they give the case over. The hacker sends electrical surges through the city and threatens to do more until they do what he wants. He arranges a meeting and wants John to deliver the case.
The police watch as John makes the exchange, and Avery reveals Paulette is missing. John notices a discrepant temperature display that leads to a bus which he boards. He gets off at the next stop, an electronics store, where the hacker is controlling the computers. The hacker tells John to destroy the case but John works backward to the local mall's security system, where he concludes the hacker is working from. John spots the wireless internet transmitter and then the hacker, who runs. John does some hacking of his own with a borrowed PDA and delays the man on the escalators, then goes after him and reveals it's Johansen.
Johansen reveals he hired all three men to steal the case and set them up in competition. Johansen reveals he considered Moretti's plan blasphemy and planned to stop him any way possible. Stella reveals it'll take them years to run all the bar code combinations, while Avery reveals the scientists were illegal aliens and disappeared. John figures out to scan the items in the order they'd be used to write a letter. They end up with Moretti's mental pattern, and he "speaks" to them and notes the technology doesn't yet exist. He hopes someone else will forge a path.
John goes to meet with Paulette and reveals Moretti did it for Paulette so he could "be" with her. John leaves her the case and takes off. Elsewhere, the scientists from Moretti's project turn over the comatose bodies to a member of the Phoenix organization and signs that they'll get in touch with them concerning John Doe.