A man is running from his life, climbing a fence and going through the woods as men follow him. He comes out onto the road and is hit by a car. The men retreat back into the woods as other drivers gather around the man, who is dead.
At The Sea, John is proposing a new contest to Digger, who sees the man on the television and recognizes him as Jay Dougan, his blood brother from childhood to when they served in Special Services together. He shows John a photo of Jay, who John sees in color.
John reviews the other people he's seen in color and wonders what Jay's connection is, and Digger insists John come with him. They drive north to the nearby town of Northam and talk to the coroner and Sheriff Ash. Digger IDs Jay's corpse and John notices that he can't see the body in color. John notices aluminum oxide on Jay's shoes and Digger determines Jay is missing his Special Services medallion. Out on the highway, John notices Jay's medallion (in color) in the tree line and Digger spots a trail. They follow the trail, unaware that the same men that followed Jay are watching them.
They go through the woods and find the Seneca Institute, a privately run institute that cares for gifted individuals suffering from breakdowns. An unhelpful guard refuses to let them in, even in the face of a bribe. They go back to check the body and John sees the enamel on Jay's teeth are gone and there is a number tag in his tongue. The sheriff doesn't believe them and already has a patient list from the Institute, and Jay wasn't on it.
They go back to their hotel but notice someone following them. They chase the man into a truck lot but lose him. John impersonates a psychiatrist to get into the Seneca Institute and brings Digger in as a "patient." John has to see one of the head doctors to check in Digger, a doctor who knows the psychiatrist he's impersonating. Digger is checked into a temporary room while John snoops around and finds a room in the secured Ward 5. Digger sneaks out and gets to the security room and makes a call to distract the guard so John can get in after bypassing the keypad.
John sneaks in and sees a variety of patients acting strangely, including several who are receiving drug injections to become "receivers" and see things at a distance through mental sheer power. John spots another patient, who he can see in color. He goes in and talks to the patient, a blind man named Michael who is also a seer. The doctors spot Digger's absence as he meets with John and Michael.
They manage to smuggle him back to their hotel room where Michael reveals he's been at Seneca since he was 15 with a fever that blinded him. He's tagged on the tongue the same as Jay and reveals that Ward 5 is for the homeless, the junkies, and he and Jay were together with a "new lady" and they had to stay together to get the whole picture. Michael believes they were spying on someone but doesn't know who was in charge. To calm down, Michael plays "My Funny Valentine" on the harmonica, much to John's shock, and then says someone is watching them. Michael directs them to the clock on the wall, where they discover a hidden camera.
John figure the camera is short-range and they go outside and identify a truck and open it to find…Sam of the NSA (from "Ashes to Ashes"). Sam denies any involvement with Seneca and tells them Moretti (from "Save…as John Doe") created Seneca as a facility to help the government creating psychic remote viewers. The government terminated the contract but they believe someone is funding the operation again…someone that could be Phoenix.
They turn down Sam's offer to help and go to the hotel room only to find Michael is missing but has a left a piece of paper with a "5" on it. At Seneca, the Doctors lock the remote viewers in and prepare to set the place on fire to cover their tracks. John goes in to find Michael and frees the trapped patients but can't get to Michael in another wing. Sam gets John out and they can only look on as the Institute burns down.
Back at The Sea, Sam meets with John and reveals Seneca was connected to a Korean terrorist group looking for dirty nuclear materials to make bombs. Sam extends John an offer to join the NSA and leaves. Digger makes sure Jay gets a soldier's burial and vows to protect John no matter what, the way he failed to protect Jay.
At a secret facility, remote viewers including Michael are being wired up by the Trenchcoat Man and used to monitor John's activities. The mysterious Stocking Cap looks on as they begin to scan John's life