Director: Allen Coulter
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.
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.
The special effects of the four-headed angel weren't finished until literally hours before airtime.
The confession sequence that can be seen throughout the episode, was a last minute alteration as it wasn't in the original script. When the first cut of the episode came in, the producers realised that certain aspects of Scully's journey weren't coming through. Thus they decided to add an 8-page scene to flesh out the emotional journey that Scully goes through.
Scully: Bless me, Father, for I have sinned. It has been several months since my last confession.
Priest: You have a sin to confess?
Scully: Father, I’m an FBI agent. I’ve taken it as my code and purpose to uphold the law … to save lives.
Priest: And now your work has come in conflict with your faith.
Scully: In a way. I was here for Easter services last week and Father McCue approached me for my help.
Priest: Why did he come to you?
Scully: Because there was a family that he felt needed my help. But it was more than that. Father, I had a daughter who died … A strange and sudden death several months ago.
Priest: Father McCue thought that by helping these people you might in some way help yourself to come to terms with your grief.
Priest: But you haven’t.
Scully: (crying) Father, I told you that I had a sin to confess … But the sin of which I’m guilty … I’m not sure if you can offer forgiveness.
Priest: What is the sin?
Scully: An innocent girl is dead because of me. I could’ve saved her life, but I let her die.
Scully: What so you mean?
Mulder: Just got a look at that body they wheeled out of here. You’ve been holding out on me. Scully: Mulder, it’s not what you think. I - I didn’t want to involveyou. I got asked to look into this as a favor for a family.
Mulder: Dara Kernof’s family?
Scully: You found Dara’s records?
Mulder: No, those are her birth records. The adoption records have been sealed.
Scully: I think one of my questions has already been answered. Dara was a twin.
Mulder: No. Actually she was a quadruplet – one of four girls. Was this, uh … cross found like this?
Scully: Uh, yes, as far as I know. Why?
Mulder: It’s inverted. Upside down. That’s a protest, a sacrilege against the church.
Scully: Put there by whom?
Mulder: It’s your case, remember, Scully? Do you have any suspects?
Scully: Not as of this time.
Mulder: Could the, uh, the victim have placed it?
Scully: Uh, it’s doubtful. Paula Koklos was severely impaired, physically and mentally – as was Dara Kernof.
Mulder: And they both died the same way?
Scully: It appears that their eyes were burnt out. Their bodies frozen in a position of prayer.
Mulder: Their physical deformities could account for that.
Scully: They might.
Mulder: Look, Scully. I know you don’t really want my help on this, but can I offer you my professional opinion? You’ve got a bona-fide, super-crazy, religious wacko on your hands.
Scully: What makes you so sure?
Mulder: The mote in the eye, the eyes as windows to the soul, an eye for an eye – he’s working from ancient scripture … ancient text … Maybe even the Bible. He may even think he’s doing God’s work.