Tom awakes to a strange Kyle who is exceedingly happy, and arrives to work at NTAC that morning to standing applause from his co-workers. Diana is perplexed at Tom's fantasies, assuring Tom that no one has ever "come back" in a ball of light. Tom questions Diana and attempts to understand what has happened. NTAC raids the "Jordan Collier Museum of Art".
Tom and Diana are back at the office, Tom attempts to do a search on the 4400 but finds nothing, Tom tries looking for the 4400 individuals themselves, but discovers that most of them are deceased and were never taken.
Nikki and Danny announce to Tom that they are engaged, and Tom finds out that he is married to a woman named Alana. Jarred, Tom is unable to piece together what is wrong.
Diana finds Tom sleeping at the 4400 centre turned art centre and proceeds to sneakily sedate him; he is then taking to a physiological ward. Alana reveals to Tom that none of this is real and that he needs to play along. 72 hours later Tom reveals to the doctor that he knows his behaviour is totally out of line, and he wants to apologize and fix it.
Tom and Alana meet up to "see if they can figure out what the hell is going on." Tom speculates that Alana may be the cause. Alana shows Tom that her life has been erased.
At the Collier Museum, Tom wanders away and looks through a door's window, seeing a covered table in the middle of the room. Tom walks into the room and is about to lift the cover from the table when he hears his name called. The scenery around him drops to complete darkness, Tom then awakes to Alana shouting and nudging him, Tom reveals to Alana he needs to get back to the mysterious room in the museum.
One month later, Diana brings Tom a coffee wondering what he is doing looking at art so much. Diana wonders why Tom would want to get back the bleakness of "his reality," and attempts to get Tom to make the best of the life he has got.
Tom returns home to a worried and upset. He and Alana contemplate if they will ever get back. As they talk, they embrace, kiss, and then make love. As the scene fades from their bedroom, they are taking the first steps towards psychological and emotional acceptance that they may never return to their previous lives.
Eight years later, Tom is preparing his suit, putting on a bow tie, and Kyle tells his father about life as a resident surgeon. Tom and Alana are going to renew their vows; she affectionately calls him "Thomas". They contemplate on their old lives during a dance at the reception.
Nina reveals to Tom her plans to leave NTAC to enter the private sector, and discloses to him that she has been asked to present the name of possible replacements. She will be giving only one name: Tom Baldwin.
At the Collier Museum, Tom returns to the door where he first saw the table. After eight years, it has returned. Tom believes it may be a way back, but Alana asks Tom if he really wants to go through the door. They both leave and go home, leaving the door unopened.
Back at his house, Tom has a nightmare about his son Kyle, awakes in a sweat, and returns to the museum. The door is still there. He walks through it, to the table, and lifts the cover. Underneath is Alana's body. An image of Alana congratulates Tom and reveals that they are in the future place where the 4400 where given their abilities. The future gave Alana her ability -- creating a virtual reality environment -- as a sanctuary for Tom, and the Alana he is speaking to is part of the program they instilled in her. In order to return to reality, the real Alana must will-out the virtual world, but when Tom tells her about this, she questions whether they should, even though Tom was assured that their feelings for each other will carry over.
Tom and Alana host a small get-together to say goodbye to their friends and family, and to tell them how much they love them. Tom tells them they are not going far, and gives a toast, Alana then begins willing things out of their virtual reality.
Back at NTAC, Tom awakens to Diana asking him to email her a file. Tom asks Diana if the ball of light really happened, Diana assures Tom that it did -- they'd just interviewed a 4400, Alana Merava. The eight virtual years had passed in the blink of an eye. Tom thanks Diana, and runs off to catch up with Alana. Outside, she is walking away, and Tom shouts to her. She stops, turns around, and smiles at him: "Thomas." They embrace.