Dr. Gardner meets with her new psychiatric patient, Johnny Morgan. Johnny explains that he came to her because she advertises her ability to stop compulsions, and he wants to stop his. She assumes that he's talking about masturbation at first, but Johnny explains that he started skinning dead cats when he was a small boy. His foster parents kicked him out and he drifted from one home to another. Johnny soon realized that killing animals was better than skinning them after he found them dead. When Gardner asks if he still skins animals, Johnny insists that he doesn't anymore. He explains that when he was in prison, he read a great deal and learned that killing animals is a predictor of psychopathic behavior.
Realizing that she's in over her head, Gardner says that she may not be able to help him. However, Johnny insists that she has to and that the voices in his head are telling him to find out who his birth parents really were. He explains that he rented the home where his father lived and admits that the voices are telling him to skin women.
In the house's basement, Johnny tells Teresa to stop screaming so that he can work in peace.
Johnny tells Gardner that he made a mess of his latest victim because he lacks his father's medical training. As she stares at him in horror, Johnny tells her that his real name is Thredson, not Morgan, and that he's the son of Bloody Face.
Mary Eunice has Lana brought to her office and shows her the report confirming that the report is pregnant. She asks if Lana is still insisting that Thredson raped her and Lana, realizing no one will believe her, says that it must have been a hallucination caused by a concussion from the car crash. The reporter insists that she isn't going to keep the baby but Mary Eunice takes great pleasure in informing her that they will help her deliver it and then put it up for adoption within the Catholic Church. When Lana says that Mary Eunice is worse than Jude, the nun tells her to watch her mouth and threatens to restrain her. Lana apologizes and starts to leave with the report... and passes out.
Jude wakes up in a Briarcliff bed, strapped in, and Howard comes in and tells her that she murdered a man. She insists that Emerson tried to rape her, but Howard tells her that she cut Frank's throat. Mary Eunice, Arden, and Emerson all testified to the review board that Jude killed Frank, while Howard and Sister Claudia confirmed that Jude was acting irrationally, insisting that Mary Eunice was possessed by the Devil. Finally, Emerson told the board and Howard that he regretted killing his eighteen victims but hopes to find redemption and apologize to his victims when he arrives in Heaven. The monsignor tells Jude that she'll be stripped of her clerical standing and spend the rest of her life in Briarcliff, then walks out.
In the kitchen, Lana is baking bread when a guard leaves a wheeled rack of hanging clothes outside the door.
Howard goes to Jude's formers quarters and notices her red lingerie sticking out of a box. As he examines it, Mary Eunice comes in and explains that she's packing Jude's things and was shocked to find the lingerie there. Howard admits that he and Jude have shared the dream of seeing him Rome as the Pope and Mary Eunice agrees that he belongs there. When the monsignor blames himself for not noticing Jude's deteriorating condition, Mary Eunice assures him that he was too busy saving souls to notice. She pledges his assistance to Howard to help him save souls... and become the Pope.
After the patients are returned to their cells for the evening, Lana takes the coat hanger that she stole from the rack and twists it apart.
Lorene and another nun try to give Jude her pills. She scratches Lorene, who is happy to see her former superior reduced to a mere patient. As Lorene taunts Jude, Howard comes in and dismisses them. He then informs Jude that she has a visitor but it might be best if she doesn't see him. Unsure of who it is, Jude promises that she'll be good and Howard escort Emerson in. The patient stands over Jude and then tells her that he forgives her.
After Emerson rapes a nun, Jude has Frank restrain Emerson to his bed to give him time to reflect on his sins. She refuses to forgive him, reserving her forgiveness for the repentant, and Emerson boasts that he doesn't need forgiveness.
Howard listens to Emerson forgive Jude and says that he's on the road to redemption. Emerson kisses Jude on the forehead and leaves.
Lana goes to the infirmary and meets with Kit, who is pretending to be drugged. She insists that they kill Thredson because he's too dangerous to let live, but Kit reminds her that they need Thredson to confess and clear his name. They're not sure how to get Thredson to confess voluntarily but Lana finally gets an idea.
Arden goes to the death chute where Grace's corpse was abducted. Looking around, he finds alien footprints in the dirt.
Lana goes to the junk room and ungags Thredson, warning him that she'll smash in his face if he makes a noise. She then shows him the pregnancy results and tells him that he won't be a father. Thredson begs her not to give their child away, but Lana tells him that she will do worse. She takes out the coat hanger and tells Thredson that she'll give herself an abortion and kill the child. Desperate to have a child, Thredson says that he can change and that Lana owes him, but she says that she can't trust him because he's a sociopath. Thredson promises that he can and Lana tells him to prove it by describing his victims' deaths. Thredson describes in loving detail how the skin of his victims felt and tells Lana that Wendy never loved her and was the one who had her committed.
Once Thredson describes everything, Kit calls out and tells Lana that he recorded the entire conversation. Thredson figures that Lana is lying about her pregnancy, but she assures him that she had his child... and already aborted it the night before. Disgusted, she tells Thredson that she'll come back later and cut his throat.
Kit goes to the hydrotherapy room to hide the tape, and Arden comes in looking for him. He takes Kit to his office and offers him cigarettes and whiskey, and Kit wonders why he's being friendly. Arden shows him a plaster cast of an alien footprint and says that he saw the same aliens that Kit described. He confirms that Kit had sex with Grace just before the aliens abducted her, and that the same thing happened when Kit made love to Alma. The doctor figures that the aliens are monitoring Kit and conducting eugenics experiments. What Arden proposes is that they take Kit to the brink of death so that the aliens will have to intervene. Eager to see Alma no matter what the cost, Kit agrees and they share a toast.
Lana finishes working for the day and tries to smuggle out a knife. However, Carl the orderly doubles back and catches her, relieving her of the knife.
Howard goes to the chapel and finds Emerson praying to God. Emerson wants to seek redemption and Howard considers the political possibilities if he can bring Emerson into the Church. He unmanacles Emerson and baptizes him in the font... and Emerson grabs the monsignor and drowns him until he passes out.
Lana convinces a nun to take her back to the room and then takes the coat hanger out from under her mattress. She tests the edge on her pillow and then goes to the junk room. However, there's no sign of Thredson. When Lana runs out into the halls, she finds Mary Eunice waiting for her The reporter realizes that the nun freed Thredson and wonders why. Rather than answer, Mary Eunice takes the coat hanger and tells Lana that her attempt to abort Thredson's child failed. Lana wonders how she knows and Mary Eunice tells her that not only does she know, but she knows it's a boy.
Dr. Gardner's next patient comes in and calls to the psychiatrist. She sees the doctor sitting in her chair, turns it around, and discovers that she's dead. When the patient hears a noise behind her, she turns and finds Johnny waiting.
Jude enters the common room and approaches Lana, ignoring everyone's stares. Lana is shocked to see the old nun in such poor condition and Jude tells her that they did the same thing to her that she did to Lana. She asks for a cigarette and then apologizes to Lana, admitting that what she did was wrong and immoral. Lana accepts her apology and Jude promises to make up what happened by getting Lana out of Briarcliff. The reporter doesn't trust her and Jude promises her that she'll earn her trust. She then gets up, goes to the record player, and smashes the constantly-playing record.
Arden prepares a dose of potassium chloride and explains to Kit that it will temporarily shut down his heart. He will then use a combination of atropine and adrenaline to bring Kit back after two minutes. Kit says that he's scared and Arden admits that he's a bit apprehensive himself. He injects Kit and Kit convulses and then dies. The lights flicker and Arden runs to the light. It leads him to a cell and the doctor is surprised to find Pepper and a very pregnant Grace inside. Pepper tells Arden that it won't be long and then that she'll look after Grace until she gives birth. Arden hesitantly reaches forward and touches Grace's stomach.
When a janitor goes to the chapel, he's shocked to see Howard crucified on the hanging cross. He runs out, yelling for help, and the Dark Angel arrives and tells the monsignor that she's there for him.