American Hugh Potocki enters the airport in Mumbai, India on his way back home. A local beggar with no legs follows him on a wheeled cart into the restroom. Potocki is yanked out from under the bathroom stall by an unseen force. Later, Potocki arrives at his hotel in Washington, DC. A bellboy brings his luggage with the beggar's cart strapped on. Potocki sits on the bed and his eyes glaze over with blood. Another pool of blood flows from his body, staining the bedspread. Scully and Doggett investigate the crime scene at the hotel where Potocki's body was found. The agents spot a small, bloodied handprint, about the size of a child's, on the bed. An autopsy reveals Potocki suffered massive abdominal tissue damage. Scully is unsure whether something went in or came out of his rectal wall. There is no evidence that the man had been smuggling drugs, but a decay analysis does prove that he had already been dead before he left India.

Mrs. Holt, the principal of Fairmont Elementary in Maryland, interviews a normal-looking man for a potential job as a custodian. Yet she does not really see that the person sitting across from her is the legless beggar. A fight breaks out in front of the school between seventh-grader Trevor and the younger Quinton. Quinton's father arrives in time to break up the squabble. The mysterious new custodian watches from nearby. Meanwhile, Doggett traces a similar death in India several days earlier that involves another heavyset American businessman. Scully introduces the idea that a living being is using these victims to stowaway by freely entering the bodies. Doggett doesn't readily accept this notion.

Later that night, Quinton sees the beggar's reflection in his bedroom mirror, but his father dismisses the boy's fears as merely a nightmare. When the father goes back downstairs, the beggar man is there. Hearing a scream, Quinton runs down the stairs to find his father dead. The man's eyes are filled with blood. Scully and Doggett investigate and Quinton tells them that he saw a man with no legs. Finding the identical small handprints as in Potocki's hotel room, the agents suspect the same killer. Yet Quinton's father showed no sign of abdominal damage. At the autopsy, the man's stomach is distended. Scully slices into the body, and a tiny hand reaches out through the incision. Scully jumps back, and grabs her gun. Whatever was in the body has disappeared, leaving a trail of coagulated blood across the floor. Scully follows it to a closet, but sees nothing inside. However, the beggar man is in the closet. Somehow he hodes his presence from Scully. When Scully and Doggett consult with Chuck Burks, he explains that there are siddhi mystics who have the power to manipulate reality. These Indian mystics, however, are religious and committing murder would endanger their souls. Scully shows him a report of an American chemical plant that killed many people in India, one of whom is the son of a holy man. Because siddhi mystics pass their skills from father to son, and his only son's death effecetively ends his legacy, Scully questions whether this man is out for revenge.

Trevor tells Quinton that he may know who killed his father. As he walks down the street, Trevor hears the squeaking of the beggar's wheeled cart, but no one is around. His mother, meanwhile, sees her son's body floating in the backyard pool and dives in after him. As she gets closer, she realizes that it is not Trevor but the beggar man. Scully and Doggett later scrutinize the woman's blood-filled eyes and question how her death fits into the case. Trevor returns home and tells the agents that the "little man" followed him. They call the janitor in for questioning, but he does not speak. Chuck sets up a video camera and focuses it on the janitor. The camera shows there is no one sitting in the interrogation room. They realize their suspect may be anywhere.

Mrs. Holt sees the custodian at the school later that night, but he does not answer her when she calls out to him. The principal immediately calls Scully. Trevor and Quinton lie in wait in the school building. When the beggar enters the janitorial closet, Trevor tosses bottles of chemicals on him. Yet the shattered glass seems to have hit nothing and the beggar disappears. Instead, the beggar chases Quinton in to a classroom with windows that won't budge open. Trevor is outside the window, yelling to his friend that he will get help. Suddenly, Scully and Mrs. Holt enter the classroom but they can't see the beggar man. He has transformed himself into Trevor. Quinton pleads with Scully to shoot at what she thinks is Trevor, but she is unable to fire at a child. Doggett arrives outside and hears gunshots. He runs in the classroom, with Trevor following him. The little beggar man lies dead on the floor.

Later, Scully is still shaken by the experience. She tells Doggett that she was unable to trust her own eyes, but fired her gun because the boys saw the truth. She realizes that it is what Mulder's open mind would have seen. "Maybe if I could see through Mulder's eyes I could understand," she says.

The beggar man, still alive, rolls his cart in an airport in pursuit of another passenger.