While John uses his knowledge to make even more money selling pork bellies, Karen is poking around his apartment as his new assistant. She breaks into his secret office where she finds his notes on his background. John comes in and catches her at it – he gives her what he knows of his back story and swears her to secrecy.
At a construction site, the workers open a barrel…and find a skeleton inside. Frank leads the investigation and determines the body has been there for 30 years. He checks with Stella and finds that a Steven Prescott owned the site at the time. They bring up a license picture of Prescott from 35 years ago – he's a dead ringer for John now.
Frank and Avery call John in but he has no explanation but shows someone could easily have hacked the DMV records. All they can find is Prescott's ex-wife and John insists on investigating since he's involved. Miss Prescott had a stroke five years ago and can't speak – the nurse says she doesn't have any personal items. Miss Prescott does see John's face…and stutters out "murderer."
Karen suggests that John might be a time traveler and takes him to a Professor Hillman who specializes in such theories, and suggests according to his theory a time traveler would have to have their memories wiped to prevent a paradox. Hillman suggests John undergo a MRI – when he does so there's interference to the magnetic field. John tries to get out and hits his head. John gets a flash of color and staggers off. Karen catches up to him at his apartment where he uses a metal detector and finds that his brand is metallic.
John continues to get color visions of what appears to be a woman's face, followed by memory blackouts. He also starts to see flashes of things in color all around him in real life as well. Franks shows up and reveals they've identified the skeleton as Prescott's maid. Further, Prescott appears to have just appeared in 1960 and has no previous history, and no history since shortly after the maid's death. Frank takes John along to see the cousin of the murdered maid and they chat about Frank's marriage on the way.
The cousin, Vanessa, claims Prescott went underground and fled the country, and John wonders why she knows Prescott killed her. Vanessa reveals Prescott found out the victim, Elizabeth, had a baby, a son. She put the baby up for adoption and only has some pictures of the baby – she never kept track of the child after that. John comes back to his apartment to find that Karen has been decorating the place – he's not too thrilled. He does suspect he might be the missing child and Prescott is his father. John plans to go see Vanessa on his own but before he leaves he has another vision/blackout…and wakes up in a pool of blood, next to a murdered Vanessa.
Frank brings John in for interrogation and doesn't get any answers, but he believes in John's innocence and asks Avery for more time. She refuses to go out on a limb but John convinces Frank to let him recreate the crime scene down in the lab. John proves that he would have been covered in blood to commit the murder and he wasn't – Avery gives him 12 hours to find the real murderer. As they leave Frank's mom shows up with their children for their scheduled visit and John finds himself oddly comfortable with Frank's kids.
John and Frank check out the body and discover a plant that doesn't grow anywhere near the area. They check out the oil drum and figure out it's a wine fermenting tank. The trail leads to a vineyard and its owner, William Leverton. They figure Prescott stole a dead kid's ID and took over the ID. Frank calls in backup and they go after Leverton at his home. They find an elderly man confined to his bed on a respiration system under a nurse's treatment.
John confronts the man, who can barely move. When he touches him he gets another vision of water and a woman, just like before. Then he wakes up in the car after suffering another blackout. John remembers that the respiration system was still on the factory settings and asks Frank to take him back. They go back to the house and find Leverton/Prescott and the nurse are gone. John finds a ticket confirmation and they head for the airport. Under John's direction of traffic signs and alternate routes, Frank manages to intercept Leverton and his car inadvertently goes off the road and into a propane tank where it's destroyed.
There's not enough of Leverton left to run a DNA test, but John is cleared of Vanessa's murder. A week later, John's blackouts and visions have ceased – he's upset since they may have been a window to his past that he no longer has. He's left with more questions then answers but he affirms that he and Karen are friends. John gets a headstone for Vanessa and leaves flowers at her grave.