Thomas Veil – quite literally – loses his identity one night over dinner and begins to mentally unravel when he discovers his wife is part of whatever's happening. Placed in a sanitarium, he slowly realizes that he's actually the victim of a massive conspiracy connected to a photograph he took entitled "Hidden Agenda".

Attempting to avert his unknown attackers, Veil uses Dr. Bellamy's driver's license and credit cards as he sets out on a desperate search for answers to who has stripped away his entire life. Before long, he's presumed to be the missing Bellamy, tracked down and taken to the enemy's headquarters for Western Operations. There, "Dr. Bellamy" is instructed to make one of their subjects, Ellen Combs, comply with the same "conditioning" procedure administered to Veil.

In his search for why someone wants the negative of "Hidden Agenda", Veil enlarges it and detects details that lead him to a remote Georgian town to seek more answers. There, he happens upon a traveling sideshow starring Derek, a blind 10-year-old billed as "The Boy Psychic", who reveals ominous news about Veil's pursuers.

Classified as the unknown enemy's first priority, the elusive Veil is apprehended and submitted into a chemically-induced hallucinatory state in which his attackers have complete control over his sense of time and space. Within their 'lab' setting, actors and elaborate sets are employed to convince Veil he's been in a loving relationship with a woman to whom he'll soon divulge the sought-after information.

After getting a job in a small-town photo shop, Veil is stunned to glimpse a picture of his wife Alyson as he processes a customer's film. He frantically pursues that customer to question where she shot the picture, but the chase lands him in New Phoenix, a haven for the disenfranchised and community of those who have, for one reason or another, lost their identity at the hands of the mysterious enemy.

While hiding out in a cheesy motel, Veil happens upon The Lenny Little Show, a public access television series in which the main character is un cannily depecting Veil's own frightening life. Struggling to understand, Veil watches as unknown forces pursue Lenny and attempt to erase his every trace. He sees the actors perform the exact same dialogue and reenact experiences he endured as recently as the previous day. Trying to grasp what's happening, Veil angrily pursues an explanation, which leads him to the strange offices of Max Webb Productions—and his tormentors.

Unsure if he's running towards something or away from it, an exhausted Veil happens upon a disabled, reclusive computer genius, Scott Hansen. The young "hacker" is able to access Veil's deleted files—the only trace of his existence—and through an intricate virtual reality session, takes Veil back to his wife Alyson and also helps him get information about his pursuers.

Searching for clues about Dr. Bellamy, Veil traces the beginnings of the mysterious man's research to a private school, The Sterling Academy. There, he gets a job as a groundskeeper and not only uncovers that the administration is programming the student body through elaborate subliminal persuasion, but exposes a murder and a conspiracy to cover it up.

As Veil's mysterious pursuers close in and are about to kill him, his life is saved by a peculiar stranger. He's thunderstruck when the man, a quirky drifter named Gus Shepard, seems to know all about his situation and, with or without Veil's cooperation, is intent on showing him the only way out of it.

In need of anything that connects him to his former life, Veil risks returning to the house and town he grew up in and, while savoring this small but significant part of his past, he unexpectedly meets the man who betrayed him twenty years earlier—his father.

While camping in Pennsylvania farm country, Veil is accidently shot by a guard for a powerful food conglomerate. Near death, he's discovered in the woods by a local woman, the beautiful Emily Noonan, who takes him to her remote farmhouse and nurses him back to health. Finally, Veil has found a safe place and someone he can trust.

At long last, Veil's torment comes to an end as federal agents locate him, reveal the identity of his enemy and disclose why The Organization, a well-funded group of political fanatics wreaking havoc with foreign policy, have been trying to destroy him. After Veil gives a sworn deposition to authenticate his "Hidden Agenda" photograph, he's reunited with his wife Alyson and his mother and is on the way to having himself a merry little Christmas, until he gets a form of 'coal in his stocking'.

A dissenter from The Organization surreptitously contacts Veil and supplies him with documentation that one of its highest-ranking members, Richard Grace, is the one primarily responsible for the decision to erase his identity.

Using information provided by his contact, a traitor within the enemy's ranks, Veil tracks down retired military man Cyrus Quinn, a renowned fanatic connected to the execution pictured in "Hidden Agenda". To gain access to the controversial and closely guarded Quinn, Veil must find a way to infiltrate the American Guard, the radical political action group he has founded.

A recurrent address in his electronic file leads Veil to a nursing home in Minnesota where he secures a job as an orderly. Initially, he finds no apparent connection to his unknown pursuers, but it turns out he's entered a covert and ominous operation, Advanced Biogenetics Lab.

Veil makes his way to New Mexico hoping to locate John Myerson, a name he's linked to The Organization. He arrives in a small sesert town which is in a clamor over several UFO sightings and is told that Myerson, a local scientist, mysteriously disappeared months earlier and is believed to have been abducted by aliens.

Veil's link, a traitor within the "Organization," directs him to the idyllic town of Darby, New York, where a suspicious degree of cleaniness, incessant hospitality and unequivocal support for one local politican prevails. As he settles among the neighborly, strangely cheerful people there, he surmises that nothing in Darby is what it appears to be.

Carefully setting the trap, Alexander Hale, the informant from within The Organization, gains Veil s confidence and persuades him to divulge the details and events surrounding the execution in his "Hidden Agenda" photograph.

After Veil's only ally within The Organization is taken away from him, he suspects the information in the palmtop computer could have been deliberately compromised all along. He debates the options and weighs the fates before using one more tip from the compact computer – the name and address of Clare Hillard, a reporter who covered the same sector where he took the now sought after "Hidden Agenda" photo.

Veil is snatched away by the enemy's operatives and taken on a manufactured "trip" down memory lane. Then, at the hand of one of The Organization's most twisted experts, he is subjected to an elaborate combination of chemicals and refracted light which triggers his advanced hypnosis.

Tom Veil is mugged by a street gang and is stripped of his belongings and, for the first time, the "Hidden Agenda" negatives are out of his possession. While Veil and the Organization both attempt to track down the gang member who stole the pack containing the coveted negatives, the thief winds up dead and Veil is a suspect in his murder.

Veil's twisted odyssey leads him back to Calaway, the Illinois psychiatric hospital where his ordeal began, and more revelations of what really happened to him while he was held there. Most astonishly, he discovers that former patient J.C. has joined the medical staff and become one of 'them'.

Veil wakes from a coma to hear the unsettling news that he was in a car accident months earlier and his ordeal of identity erasure was just a terrible nightmare. At his bedside is his ever-loving wife Alyson and his best friend Larry Levy, a man Veil swears he once saw dead and stuffed in a closet.

Just when he's at the end of his rope, Veil finds new meaning in the "Hidden Agenda" negative when he enlarges a print of it and discovers a previously obscured section. The new clues lead him to Heritage House, a research facility in Washington D.C. and its foreboding Project Marathon. There, he stumbles upon an FBI investigation and is targeted for assassination by more than one enemy.

Following up on secret information provided by the FBI, Tom finds two valuable clues: the original untouched photo of "Hidden Agenda" and a key to the safe house inhabited by the agent who gathered the data – an operative code named 'Gemini'.