In Coats Grove, Michigan, Bobby Rich, a sixteen--year--old boy, is berated by his stepfather, Phil, for not finishing his lawn work outside the house. Bobby picks up a shovel and instructs his stepfather to keep his distance. As the dispute escalates, Bobby drops the shovel and runs into a nearby orchard. Phil gives chase. Suddenly, Phil's feet are knocked out from underneath him. A short time later, Phil's wife, Patti, makes her way through the darkened orchard. She discovers Phil's body buried in mud up to his shoulders, with mud seeping from his nose and mouth. Kneeling beside Phil is Bobby, his eyes wide with terror.
Scully performs an autopsy on Phil's corpse. She discovers over twelve pounds of mud in his stomach. Her conclusion: Phil's head was forcibly held in the mud, mostly likely by his son, Bobby. She hypothesizes that Bobby may have dug the pit that trapped Phil, and, noting a rope--like bruise on Phil's ankle, speculates that Bobby may have had help from an accomplice. Mulder interviews Bobby, who claims his father enjoyed physically abusing him. Later, Patti tells Scully that, from her point of view, it appeared as if Bobby was attempting to help Phil out of the muddy orchard pit, not cause him harm. She also reveals that her son has been undergoing therapy for his anger since 1995. Later, the agents meet with Bobby's therapist, Karin Matthews. She describes Bobby as the victim of physical abuse. But Mulder expresses his belief that Bobby may not be to blame for his stepfather's death.
Bobby tells a pretty fellow student, Lisa Baiocchi, that she must stand up to her father‹ just as he had done with Phil. When Lisa returns home, her angry father demands that she stop seeing Bobby. An angry Lisa storms off to her room. Shortly thereafter, a window explodes, and a shadowy, arm--like appendage grabs Mr. Baiocchi by the throat. His lifeless body is discovered lying on the ground outside the house. Though Scully concludes that Mr. Baiocchi died as the result of being pushed out the window, Mulder discovers evidence suggesting he was pulled out the second story window. Later, the agents learn that Lisa is also one of Karin Matthews' patients. Karin tells Mulder her approach with victims of abuse is to encourage them to empower themselves‹to confront and stand up against their abuser.
With the aid of a town coroner, Mulder a small splinter of fresh wood embedded in Mr. Baiocchi's neck. Mulder matches the fragment to the living tree outside the Baiocchi home. A short time later, the agents are approached by a man named Ramirez, who holds an axe at his side. He tells the agents that the trees are all dying because of a "bad man." Karin invites Lisa to stay at her home until her aunt can pick her up the following day. As Lisa listens from her bedroom, she overhears an argument between Karin and a male voice. A curious Lisa makes her way to the root cellar, where she discovers the body of a man. Terrified, Lisa turns towards the door, only to hear it slam shut. A dead bolt turns, locking her within. She hears the unidentified man's voice refer to her as "a snoop." Later, Karin tells the trapped Lisa she must remain quiet, or the unidentified man will hear her voice.
Mulder discovers that Karin's father was pulled from the mud of an orchard twenty years earlier. He finds it strange that Karin failed to mention the coincidence. Ramirez tells Mulder that Karin Matthew's father's death brought about an end of a blight affecting the trees. Karin attributes the tale to her father's stature, believing powerful men inspire fantasy. Later, Mulder digs up Mr. Matthews' casket... and finds it empty, save for roots. When Lisa's aunt, Linda, arrives at Karin's house, Karin informs her that Lisa left for a bus station. Before Linda drives off, Lisa smashes the glass of a window in the basement. Linda rushes to her niece's aid, but she is attacked and killed by an unseen force as tree branches sway in the wind above her. Later, Bobby tells Mulder that, as part of therapy, Karin made him pretend he was Phil... and that, all along, he was never a really a victim.
Lisa hears the cellar door bolt slide. She stands up... only to realize the unidentified male voice has been coming from Karin all along. Scully and Mulder search Karin's house, where they come upon the corpse Lisa discovered earlier in the root cellar. Mulder concludes the body is that of Karin's father. Karin locks the agents in the root cellar, but Mulder forces it open. They find Lisa frightened but unharmed in a corner of the kitchen. Mulder attempts to pursue an escaping Karin, but his car crashes into an enormous tree. Karin drives to the Rich residence, where she chases Bobby into the orchard. Suddenly, Bobby is dragged downward into the mud. While attempting to rescue the teenager, Mulder simultaneously encourages Karin to break the cycle... to fight the voice inside her head. But Karin is unable. A tendon--like root snakes out of the mud and drags Mulder downward. Ramirez appears, axe in hand, and strikes Karin, killing her. Mulder and Bobby are released by the unseen force.