John and the gang arrive at The Sea from a movie showing, although the others are annoyed that John had to keep commenting on movie history. John is then hit by a painful vision but dismisses it. After the others leave, John goes for a walk but he's hit by another confusing vision of clocks and valves. Elsewhere the black-suited men of the Phoenix Organization are in a cannery and John's life is being projected up on a screen in front of the remote-viewers as the Trenchcoat Man orders that they get an increased dosage to clarify their seeing.
John seemingly wakes up and finds himself in a circle like the one where he initially woke up, although he's fully clothed. He strides out of the woods to find himself near a street where he gets more of the painful visions. He returns to The Sea and tells Digger what's going on, wondering what's happening. Digger assures John he'll always be there for him.
John goes up to his room where he has another vision and tries to gather information on the clocks and valves he's seeing, as well as a series of grid-lines. He realizes that the lines represent the electric lines on a topographical map, and then gets a call from Frank about an unidentifiable corpse… beneath some electric lines. John investigates and the corpse's face has been burned off with acid. They do find a small stab wound in the knife. John has another vision, while at the cannery the Stocking Cap signs to Trenchcoat Man that John is on their trail, and once he finds them, "it begins."
Nance is running the autopsy and notices the corpse's wrists are discolored. John realizes the murder M.O. is the same that the Phoenix Organization uses. He realizes the red marks are indicative of bursitis and finds a fish scale, indicating the dead man worked at a cannery, and he's been seeing assembly-line valves. John goes off on his own and checks out the canneries on the waterfront and finds one that matches his visions. However, the place is deserted and he finds a single piece of paper flower that he can see in color. It has the same power line sketch on it that he saw. Sam the agent confronts him at gunpoint but they quickly realize they're working (more or less) together. Sam lost his man on the inside, who John identifies as the corpse. The Trenchcoat Man comes in and quickly runs away. Sam and John give chase and the man gets to a kit where he tries to inject himself with liquid cyanide. They manage to stop him and Sam takes him to his agency HQ for interrogation.
Sam asks for some consideration from John and says he's been protecting him from his superiors. John finally relents and they shake on it, then interrogate Trenchcoat Man. He's been seen all over the world and is connected to Yellow Teeth and the mysterious unidentified Stocking Cap. Trenchcoat Man is unimpressed even after John loses his temper and tries to strangle him. Sam hustles him out of the room and John reveals he's figured out that Trenchcoat Man can hear. They rig up a sonic system and broadcast high-frequency noise. Trenchcoat Man initially tries to bluff it out but John cranks up the noise until Trenchcoat Man cringes in pain. He says John is one of them but he doesn't know what he really is. He says in Sanskrit and then Latin that John has been "chosen" and when it is time, he will complete his destiny. He feels John should have been told the truth, and Yellow Teeth was the one who tried to fool John. John wants to know where Theresa is, and Trenchcoat Man gives away that there are others like her. Sam figures that Michael is still alive and is being used by Phoenix. In the interrogation room, Trenchcoat Man manages to open his handcuffs telekinetically and make his escape. He's gone before they realize he's gone.
Sam takes John to a cabin where a man, Lucas Doya, is working on model buildings. Doya doesn't want to get involved until Sam mentions that John is a "Class 1." Doya founded the remote-viewing project for Langley and then retreated from civilization. After Sam leaves, Doya blindfolds John and offers him two stones, one burning hot and one cold. John picks the right one but only through deductive reasoning, which Doya knows. Doya has John participate in a series of exercises to help him develop his abilities. John sculpts a model pyramid to indicate where a coin is hidden--under one of Doya's building models. Doya then has John start painting and he starts to get a fix on Theresa's vision as the cans explode. He paints out a tunnel, a copper mine near water, and realizes that Theresa is alive.
Sam assembles a tactical team and Jim insists that he, Avery, and Hayes go with them. Sam agrees. At the copper mine, the men in black are working as the remote-viewers Michael and Theresa continue to probe John's life while Stocking Cap looks on. They start to get an image and Stocking Cap orders everyone to stop working and the remote-viewers both draw a picture of… the Vatican. Trenchcoat Man arrives to announce they've been betrayed and the remote-viewers have warned John.
The tactical team bursts in and Trenchcoat Man kills Michael. Stocking Cap hauls Theresa away and John spots him. While the tactical team secures the others, John goes into the mines after Stocking Cap, who shoves a mine car at him. John ducks it and continues to pursue, and Stocking Cap climbs up a ladder to the surface. John manages to pull Theresa away but as John looks up at his escaping nemesis the cap falls off and the man is revealed as… Digger.