Adam Farmer narrates as he pedals his old bicycle from Monument, Massachusetts, to visit his father in Rutterburg, Vermont. He carries a package for his father.
In the first of a series of undated taped transcripts between Adam and a doctor named Brint, Brint asks Adam to remember his earliest memories. In a third- person narration, Adam describes taking a long, exhausting bus trip with his mother and father in the middle of the night. The Farmers end up in a different house, where everything felt different.
During his bike journey, Adam gets directions to Rutterburg from an old man at a gas station. Adam tells him he will stay at a motel in Belton Falls that he once stayed in with his family, and he lies that he is visiting his father in a hospital.
Brint brings up the name Paul Delmonte, whom Adam does not know.
As Adam pedals along the road, he sings the children's song "The Farmer in the Dell," which was the Farmer family theme song. Adam's fears are realized and he is confronted by a ferocious German shepherd at the bottom of a hill, but he manages to ride past it.
Brint asks Adam about the mysterious "clues" he alluded to earlier in their dialogue. Adam mentions that the dog may be a clue. Adam remembers walking to the library with his father when he was nine. His father suddenly led Adam on an alternate route through the woods, where father and a vicious dog fought. Adam remembers that something was strange about his father's flight into the woods.
Adam tells Brint about his girlfriend, the mischievous, talkative, but ultimately sensitive Amy. He remembers a day Amy called to tell him that, while at her father's newspaper office, an editor had dropped in for a visit from Rawlings, Pennsylvania, where Adam had told her his family had moved from. She said that the editor did not know of a Farmer family. Adam lied to Amy that they only lived in Rawlings for a few months, but he became more curious about his family's past.
Brint asks Adam if he thinks his father lied to him about coming from Rawlings, but Adam says no. Adam remembers the one time he investigated further. His father kept official documents in his bottom desk drawer at home, and Adam unlocked it one day while his father was outside. He found his birth certificate from Rawlings. He also found another certificate in a sealed envelope—for him again, but with the wrong birthday.
Adam tells Brint he thought the second certificate was a mistake. But he remembers spying on his parents and wondering what secret they seemed to be hiding that made his mother sad and closet herself in her room all day. The only day she was happy was on Thursdays, when she had her "special" telephone hour at night that Adam was not to interrupt. Adam often wondered whom she would be calling, as she had no friends, and they had no living relatives, as his father had told him before. One Thursday night, Adam eavesdropped on his mother over another phone. He overheard an older woman named Martha asking about her nephew, Adam, and realized that his parents had lied to him.
Resting from his bike ride and eating at a Carver diner, Adam is harassed by a teenager, Whipper, and his two cronies. Adam leaves the diner, package in hand. Before leaving Carver, Adam places a call to Amy. A man answers and says there is no Amy at his residence. Adam sees Whipper and his friends coming, and makes a quick getaway on his bike.
Adam brings up someone called the "gray man" to Brint. He is not sure who he is, but knows that he is an important clue. Brint brings up Paul Delmonte. Adam asks if he is the gray man, and says that when he was brought up earlier, he was bluffing when he told Brint he did not want to talk about Paul. He actually does not know who Paul is.
Adam pedals outside Carver. A car, driven by Whipper and his friends from the diner, knocks him into a deep ditch next to the road. A kindly old man and his paranoid wife help Adam out of the ditch and give him a lift to a town near Belton Falls.
Adam tells Brint he remembers who the gray man is now. He was someone his father called Grey, who was always there in their lives, but seemed like he was invisible, which is why Adam called him the "gray man." Grey came to their house once or twice a month, on Saturdays, to talk with his father in the cellar. He remembers one Saturday when he tried to spy on his father and Grey, but the cellar was soundproof. His father, unbeknownst to him, saw him, and later Adam spied on his parents as they discuss Adam's growing suspicions.
With Brint, Adam says that his father told him his real name was Paul Delmonte that that Adam Farmer was a fabrication. His father revealed that his own real name was Anthony Delmonte, and that he had been a reporter in the small town of Blount, New York, for the Blount Telegrapher. He was soon promoted, and later uncovered certain important documents at the State House in Albany which linked officials in the corrupt state and federal government to organized crime. Anthony testified in Washington, D.C. before a closed Senate committee, and in return he was promised protection and his identity kept secret. For a year, he hid in hotel rooms and only occasionally visited his guarded home.
Adam says his father did not tell him everything about the situation so that Adam would be protected against betrayal if he were questioned. Adam tells Brint that his father finally returned to his job in Blount, thinking that the whole ordeal was over. After near-fatal brushes with a car bomb and a hired killer, Anthony realized he was not safe.
Adam tells Brint that Grey was one of the first men behind a new government program to protect witness who testified against powerful organizations, called the U.S. Department of Re-Identification. Grey's men had foiled the two murder attempts, and when Louise received a threatening phone call one night, Anthony reluctantly agreed to join the department. Grey relocated them with new names but kept them in the Northeast so they would not stand out. Grey arranged for the newspaper to report that the family had been killed in a car crash.
Back in his journey, Adam emerges from a drugstore in Hookset to find his bike has vanished. He looks for it in a deserted area. He spots a large man with a Southern accent, Arthur, who is virtually encaged in the second-floor fire escape of a nearby building. Arthur tells him that Junior Varney took the bike.
Brint presses for more specific details about Anthony's testimony, which Adam says his father did not have time to tell him about.
Adam remembers asking his father more about the transition. Anthony explained that it hurt to give up journalism for insurance, but it hurt Louise more, as she was attached to Blount. He told him that Grey comes to Monument to update him on developments, ask about any forgotten details about the case, and bring bonus money. He says that, although the evidence he gave has been used, no one knew if he had divulged all possible information, which is why he believed Grey checked in for more details, even though he always tells him there is nothing more.
Brint asks several times about Anthony's information, but Adam says he never questioned his father, and is taken aback by Brint's aggressive requests. He thinks that Brint may be one of his father's enemies, but he acknowledges his dependence on Brint for recovering his memory.
In the first person account of Adam's journey, he fights Junior Varney outside his house, reclaims his bike, and rides away.
Adam tells Brint a memory of the time the Farmers had to leave town for a few days, as one of Grey's men had overheard a conversation on a wiretap in which Monument and the next day's date were mentioned.
On the bike trip, Adam finally reaches the "Rest-A-While" motel in Belton Falls, the one he stayed in with his parents last year. It appears closed and deserted. He calls Amy on a pay phone. Adam is connected to the same man as before, who says he has had the number for three years. A gas station attendant tells Adam the motel has been closed for a few years.
Adam describes the family's road trip to Brint. They stayed at the "Rest-A- While" motel, and the next morning headed out to another town. Thinking a car was following them, they pulled over to the side of the road as if to admire the view. As the other car passed, Adam's father assured them that they were Grey's men. They drove on until they reached a breathtaking view, and the Farmers stepped out of the car. Suddenly, a car came out around a curve and crashed into them. Adam was sent flying and his mother died. He heard three voices that said his father got away, but that "they" would get him. Adam saw a tall man in gray pants walk toward them. The man told the other men to keep Adam, as he may be "useful." Adam was taken by them and fell into a hazy dream.
Brint asks Adam who the man was, but Adam does not respond verbally or physically.
Adam reaches Rutterburg, the final destination of his journey. He turns a corner and sees "the hospital" and meets Dr. Dupont. Adam looks out the gates and vows to ride his bike out there someday. He and the doctor walk past many of the employees and patients. They enter Adam's room, and Adam asks him if his father is dead. He fears going to "that other room" where he answers questions. The doctor does not answer, but Adam recognizes the sad look on the doctor's face that tells him his father is dead every time Adam brings him up.
Adam sings "The Farmer in the Dell" as the doctor opens up the package and takes out Pokey the Pig, Adam's old stuffed animal. Adam finishes the song, which ends with "The cheese stands alone." The doctor calls him Paul, and Adam wonders who that is. He knows there is another name, but he cannot think about it. He knows who he is, he thinks, "I am the cheese."
Brint files his annual report on "File Data 865–01," the information Adam's father may have known about, with references to "Subject A" (Adam), "Personnel #2222" (Grey), and "Agency Basic Procedures." He says it was impossible to elicit the "suspected knowledge" of Adam sought by "Department 1- R." This is the third annual questioning of Adam, and he continues not to reveal any information given by "Witness #599–6" (Adam's father). Brint issues three possible advisories for Adam's case. One, that Department 1-R revises a policy that disallows "termination" (death). Two, that the Department reinstate the suspended Grey, since it is unclear whether Grey allowed the termination of Adam's parents by "Adversaries," and "only circumstantial evidence" shows that Grey notified them of his Adam's father's location. The final advisory states that since Adam is the final linkage between Adam's father and File Data 865–01, Brint recommends that Adam be confined until termination is approved, or until he "obliterates."
The final page of the novel reprints the first paragraph of the book, where Adam begins his journey to Rutterburg.