It is the year 1997 and a young man by the name of Johnny Truant has stumbled upon a chest full of papers (scraps of papers). The chest belonged to an old man named Zampano. Johnny's friend, Lude lived in the same apartment building as Zampano. Day after day Zampano held his daily ritual of walking around the apartment grounds, feeding the birds and enjoying a peaceful and quiet life. Lude and the other occupants of the apartment building noticed that Zampano was very punctual with his walks and of feeding the birds.

Johnny gets a call from Lude one day and says that the old man hasn't been seen in days. It is unusual for the old man to just disappear as he had. Johnny, out of morbid curiosity, gets in his car and meets Lude at the apartment. Once he arrives, he notices the police cars and ambulance that surround the property. The old man died alone in his apartment and no one really noticed until Lude mentioned that he hadn't been around for a few days.

Lude and Johnny enter the old man's apartment after the police and ambulance leave and Johnny finds deep scratch marks around where the old man's body had been. These marks were deep and looked to be some kind of animal scratches. The old man had no scratches on his body anywhere, which Lude and Johnny found to be strange considering these scratches were just beyond where his body laid dead.

Johnny sees the trunk and opens it noticing all of the scraps of paper within. He takes the trunk home to his apartment and decides to read them. The scraps of paper contained a story, which Johnny slowly put together. The story was actually called the Navidson Record about a family who bought a house in Virginia and eventually runs for their lives from a presence that occupied the internal walls of the house.

Johnny puts the pieces of scrap paper (the story) together day after day and as each day passes, he becomes more obsessed with the story. Although, throughout the story Johnny shows us bits and pieces of his life with crazy woman and loads of drugs, bar scenes and sexual activities, he still returns to his apartment and the sordid tale of the Navidson Record. As he reads the story, he becomes less interested in the outside world. He stops eating, loses his job and is getting evicted from his apartment. He also starts hallucinating about a monster with sharp claws stalking him. He not only dreams about this monster, he sees it in broad daylight and believes it is real. Slowly he loses touch with reality and will not even venture out of his apartment, but for tuna fish and books from the library.

Parallel to Johnny's story is the Navidson family story. The actual events surrounding the couple that moves into the house in Virginia, their two children and the interior of the house that seems to change as an everyday occurrence. A hallway that was not there when the family moved in seems to appear after a few weeks. Will Navidson (the father) notices several things that just don't add up (a hallway, a door and measurements of the house that were not as they once were). The interior measurements of the home are larger than the exterior measurements are. This is simply incomprehensible to him, his brother and his engineer friends.

Navidson, his brother Tom and three recruits (Holloway, Jed and Wax) put together an exploration unit to explore the mysterious hallway that suddenly appeared in the house. The first day the men are in the hallway about an hour when they notice it is larger than they anticipated. They hold a second, third and fourth exploration, but when the fourth exploration lasts more than five days they begin to fear for the worst. Holloway loses his mind and starts shooting at Jed and Wax. Jed dies, but Wax survives. Navidson performs a rescue mission with his brother Tom and a friend named Reston who is in a wheelchair. They recover Jed and Wax and later capture Holloway's video camera and discover that he commits suicide within the vast hallway.

Navidson and his family flee the house for their lives returning to New York. Tom dies during the escape. Navidson later returns to Virginia leaving Karen and the children in New York. He and Reston continue researching the house. When Reston thinks Navidson has had enough research he suggests he return to his family in New York. Navidson leaves the next morning while Reston sleeps and returns to the house instead. He isn't seen again for six months.

Karen eventually returns to the house in Virginia to find Navidson. She and Reston search every corner of the house and don't find Navidson. Although his car is in the driveway, he is nowhere. Karen stays for days on end and finally one day his gear and videos appear in the children's room. Later, Karen ventures in the dark room and finds Navidson. Although barely alive, he is hospitalized and recovers. The family then moves to Vermont where they continue their lives together trying to forget about the house. Johnny goes on to actually publish The House of Leaves under Zampano's name.