S5E9 · Schizogeny

In Coats Grove, Michigan, a teenager with anger management issues named Bobby Rich gets into an argument with his stepfather Phil about yard work. Bobby eventually darts into a nearby orchard to evade Phil, but the latter gives chase. Later, Bobby's mother Patti enters into the orchard and finds Phil dying, his body sinking into a mud puddle. A terrified Bobby is next to the body.

Fox Mulder (David Duchovny) and Dana Scully (Gillian Anderson) investigate the crime. Scully believes that Bobby killed his stepdad by luring him into a pit trap. Patti repudiates this hypothesis, arguing that when she arrived it looked like Bobby was trying to help Phil rather than harm him. Mulder and Scully meet with Bobby's therapist, Karin Matthews, who tells them that the boy has been physically abused. Despite the evidence to the contrary, Mulder begins to believe that Bobby is innocent.

Bobby meets up with his classmate Lisa Baiocchi. Just like Bobby, Lisa attends therapy sessions with Matthews as her father Eugene is abusive, Bobby tells Lisa that she should not take any more abuse from Eugene. When Lisa returns home her father angrily tells her to stop seeing Bobby. Suddenly a mysterious arm-like appendage bursts through the window and yanks him outside. The next day Scully examines the body and concludes that he was pushed out of the window. Mulder however, thinks he was pulled.

While examining Eugene's corpse Mulder finds a splinter in his neck, the wood of which matches the trees outside his house. While they continue to investigate the crime Mulder and Scully are approached by a mysterious man (George Josef) who claims that a "bad man" is killing the area's trees and that this had happened 20 years earlier. The blight had stopped when the bad man was killed. While this is happening, Matthews takes Lisa to her house claiming that she is protecting her. After Lisa overhears Matthews arguing with a man she journeys into Matthews' root cellar where she finds a corpse. When she tries to leave she finds she has been locked in.

Mulder later discovers that Matthews' father was retrieved from a mud puddle twenty years before the events of the episode. He begins to suspect her of wrongdoing — suspicion that is furthered after he digs up her father's grave and finds no body but a coffin full of tree roots.

Lisa's aunt journeys to Matthews' house to retrieve her niece, but is killed by Matthews who is revealed to have a split personality engendered by abuse from her own father. This has also given her power to control the trees in the area. Mulder and Scully later search Matthews' house and find the mysterious corpse in the basement pinned to the wall by tree roots — who they realize is the body of Matthews's father — as well as an unharmed Lisa. Meanwhile, Matthews goes to Bobby's house and chases him into the orchard. The agents show up soon thereafter and both Mulder and Bobby are nearly drowned in mud. The mysterious man suddenly appears and cuts Matthews' head off with an axe, ending her power over the trees.