Father McCue, the family priest who comforted Scully during her bout with cancer (see episode 5X03), baptizes Dara Kernof, a sixteen-year-old, severely mentally-retarded girl confined to a wheelchair. Later that night, as a thunderstorm rages, Dara somehow gains strength in her legs and leaves her house. Dara's father, Lance, realizes something is amiss and makes his way outside. There he sees Dara in the middle of the street, her arms raised upward, kneeling before a Dark Figure. Suddenly, lightning flashes, supernaturally bright. When Lance reaches his daughter, he realizes she is dead--her eyes gone, as if having been burned out of their sockets. The Dark Figure, however, is nowhere in sight.
Father McCue contacts Scully and asks for her help in solving the mystery of the girl's death. Later, Scully visits the Kerofs, and learns that Dara was adopted six years earlier. The girl suffered from severe spinal deformities which confined her to a wheelchair her entire life. There is no explanation as to how Dara walked out of the house, though Lance is convinced he saw the Devil standing over her in the street.
Scully and a pathologist, Vicki Belon, examine Dara's body. Belon notes her misshapen hands and feet, which contain six digits (the extra fingers having been removed via surgery). Belon reluctantly proposes that the girl was struck down by God, as if she was a mistake.
Meanwhile, a man named Father Gregory visits a psychiatric hospital hoping to visit a girl named Paula Koklos, Dara's twin sister. But his progress is hindered by Aaron Starkey, a department of social services worker, who notes that the priest's adoption petition lacks his approval. Upset, the priest leaves the hospital. That night, a man enters Paula's room. An intense halo of light surrounds the figure and wings form its back. The next day, Scully examines Paula's body, her eyes burned out, kneeling much like Dara. Mulder joins his partner and reveals he has located Dara's birth records, which show she was one of quadruplets. Shortly thereafter, Starkey reveals that Paula was about to be adopted by Gregory.
The agents pay Gregory a visit at his church. He insists he was trying to protect Paula from harm, and makes reference to an ongoing struggle between good and evil for all souls. Later, while examining Paula's body, Scully experiences a vision of Emily.
Mulder performs further research on the adoption records. He uncovers information on a third sister, who walked into a teen crisis center a week earlier and is apparently homeless. With Starkey's help, he canvases abandoned buildings in a desolate part of town. But the Dark Figure, this time sporting a hideous lion's face, finds the girl first. Mulder draws his weapon and orders a darkened figure to step into the light. It is revealed to be Father Gregory. Gregory laments that they are too late, as he found the third sister dead.
Mulder concludes Gregory is responsible for the murders. But Gregory insists he tried to protect the girls' souls from the Devil. He warns that the fourth sister must be located before it is too late. The agents step out of the police interrogation room where Gregory is being held when new information about the fourth sister, Roberta Dyer, comes to light. Scully urges Mulder to find the girl. Meanwhile, Starkey enters the interrogation room where Gregory is being held. He demands to know the location of the fourth girl. When Gregory does not answer, he is burned alive by the demon.
Mulder makes his way to the home of George Dyer, the fourth sister's adoptive father. Dyer eventually reveals that Father Gregory took Roberta away. Shortly thereafter, Scully is approached by the Dark Figure, whose head rotates, revealing the faces of a lion, a fierce bird, and a satyr. Stunned, Scully seeks out Father McCue for answers. He explains that the vision she experienced is a Seraphim, an angel who descended from the heavens and fathered four children with a mortal woman. The Lord sent Seraphim to earth to return the girls, who have the souls of angels, back to heaven to keep the Devil from claiming them as his own.
Later, Starkey tells Scully that the fourth girl is at Father Gregory's church. Once inside the church, Scully sees Starkey's shadow, which is in the form of a demon. Scully rescues the girl from a crawlspace and attempts to make her way out a back exit. A blinding white light suddenly erupts, the source of which is the mysterious Dark Figure. The fourth girl changes into the form of Emily--and begs Scully to let go. Scully reluctantly releases the girl's hand, and she disappears into the light. When the light fades, only the girl's body remains, her eyes burnt away. Later, Scully tells Mulder they should have been protecting the girls from Starkey, not Father Gregory. She also believes that no one killed the girls... but they are now in a place where they were meant to be. She concludes the incident was about letting go... of Emily.