Arden injects Kit and tries to revive him. Kit finally wakes up and asks what happened. The doctor explains that he almost died but will recover. When Kit asks if the aliens came, Arden lies and says that they didn't.
Earlier, Arden examines a pregnant Grace in his lab and confirms that the aliens healed the bullet wound. Pepper appears in the room despite the locked doors, assuring Arden that she goes where Grace goes. The doctor, unimpressed that she can now speak, figures that she has no capacity to think. He asks Pepper what the aliens put in Grace but Pepper says that she won't tell. Arden prepares to x-ray Grace, but Pepper informs him that the aliens have protected Grace and he'll see nothing.
Pepper tells him that the aliens laugh at him for his crude experiments and he prepares to cut Grace open. The former patient confidently tells him that he can't do it and when he tries, the scalpel flies out of his hand. Pepper explains that because she's a pinhead, she gets blamed for everything and no one takes freaks serious. She tells Arden that the aliens will blame Arden for anything that happens to Grace, take him away, stir his brain, and return him as a freak. Disgusted, Pepper tells Arden to go to his whore nun while she tends to Grace.
Sister Mary Eunice wheels the injured Monsignor Howard into a room and assures him that he's not to blame for trying to see the good in Leigh Emerson, who has escaped. As the nun assures Howard that she'll be sleeping nearby if he needs anything, the monsignor remembers the Dark Angel telling him that the Devil has possessed Sister Mary Eunice and God has chosen him to cast the Devil out. The Dark Angel tells him to use his rosary to block his thoughts so that the Devil won't know what he knows. Clutching his rosary, Howard thanks Sister Mary Eunice and she tells him that she'll be back later, promising him that exciting new things are happening.
In the common room, Lana and Jude watch as Sister Mary Eunice sets up a jukebox and whistles for the patients' attention. She then announces that after Jude broke the record of their favorite song, she bought a used jukebox. The nun plays "I Put a Spell On You" in honor of Jude and walks out, and Jude leaves the common room. Kit comes over and hugs Lana, and they talk privately. As Kit says that Thredson is loose, Thredson enters the common room and comes over to where Kit and Lana are sitting. He tells Lana that he hopes she passes on her courage to their child, and that she's safe as long as he needs her to give birth and breast-feed the boy. Thredson reminds Kit that he's still a wanted man and Kit dares him to turn him in. The psychologist knows better since Kit would take Thredson's taped confession with him. He informs them that Sister Mary Eunice has offered him a full-time position after freeing him and walks away.
That night, the orderlies get all of the female patients out of their cells for an inspection. Jude and Lana look at each other as Sister Mary Eunice comes in. Lana grabs her and asks if she's insane. Once the guards pull Lana off of her, the nun says that Thredson will whip the place into shape. Lana warns Sister Mary Eunice that Thredson will eventually murder her, but the nun assures her that Thredson wants the best for her... and then has the orderlies take her to hydrotherapy for a hot-water treatment.
Sister Mary Eunice asks if anyone else has a bone to pick and Jude says that she does. The nun searches the cell and "finds" a cucumber, and asks if Jude thinks of Howard when she uses it. Jude dares her to do her worst and the orderlies take her to Arden for electro-shock therapy. As the orderlies hold her down, Jude tries to get through to the real Mary Eunice but the possessed nun tells her that they'll burn the bad memories out of her. Arden applies the electrodes and lets Sister Mary Eunice throw the switch.
Later, Sister Mary Eunice goes to Howard and treats his crucifixion wounds. She assures him that the wounds are healing and says that he deserves to be canonized. Howard grabs her and prays, holding the rosary to her forehead. She throws him away and recites a dirty limerick, mentally casting the monsignor on the bed when he tries to cast her out. Sister Mary Eunice then climbs on him and starts to undress, while the immobilized Howard begs her to stop. She places his hand on her breast and realizes that it's the first time, and says he should feel it at least once before he dies. As she rapes him, Howard begs her to stop but finally gives in. As he finishes, Sister Mary Eunice turns and sees Arden watching from the doorway.
Jude staggers into the common room as everyone watches and some of the patients laugh. Lana figures that they turned the power up but admits it doesn't make her feel better. Meanwhile, Jude staggers to the jukebox and hits it repeatedly. Lana goes over and pulls her away before the orderlies can get involved, and asks the ex-nun if she knows her name. The song "The Name Game" comes on the jukebox and Jude hallucinates everyone dancing and singing with her. Once she snaps out of it, Lana tells her that her name is Judy Martin.
Arden goes out into the woods for an afternoon feeding and Sister Mary Eunice. He insists that there is no "us" and she assures Arden that Howard didn't mean anything to him. As the mutants close in, the nun suggests that they give Jude a transorbital lobotomy but Arden refuses, saying that he won't do it because she wishes it. He then takes out a gun and shoots the mutants dead, telling Sister Mary Eunice that the experiment is over. Initially shocked, Sister Mary Eunice finally congratulates him on his temper tantrum. He says that it's a farce and places the gun to his head, but breaks into tears and collapses sobbing to the ground. Arden tells Sister Mary Eunice that she can't understand what it means to have lost her, but she tells him that he's being pitiful. He asks her to have pity on him but she kicks him away and leaves.
Later, Jude is working awkwardly in the kitchen with the other patients when Howard comes in and tells everyone to come to the common room. He approaches Jude and asks her to stay there, and then admits that he doesn't know who else he can unburden himself to. Howard apologizes to her and says that she was right. He tried to cast the Devil out of Sister Mary Eunice and failed, and blames himself for not listening to Jude when she warned him. Now the nun has destroyed them both, stripping him of his virtue, and Howard wonders if he should renounce his vows. He asks Jude for her counsel, taking her hand. After a moment, Jude tells him to kill Sister Mary Eunice.
Thredson tells Carl the orderly to secure Kit in a straightjacket and bring him to his office for his first session. The psychiatrist then knocks at Arden's door. When there's no answer, he goes in and looks around for the sodium pentothal. As he searches, he hears a woman screaming and looks into Arden's lab. He finds Grace giving birth and Pepper playing midwife.
Howard is in his room praying to God when Sister Mary Eunice comes in and quotes Scripture to him. She asks if he's having regrets and asks if he's ready for round two. Howard backs away, insisting that they won't repeat that indiscretion again. Sister Mary Eunice, reading his mind, realizes that he wants to kill her and is praying for the strength to do it. She points out the potential murder weapons in the room and then dares him to strangle her like he did with Shelley. Howard tries to deny it but Sister Mary Eunice says that she knows everything he knows after what they've shared. She promises him that they'll rise together through the Church hierarchy and he'll have all the power he wants. Howard says that she doesn't know him but the nun says that he's weak and she's strong enough for both of them. After declaring that Howard belongs to her body and soul, Sister Mary Eunice walks out.
The monsignor follows her and says that the Devil couldn't even defeat Sister Mary Eunice, whose purity is still alive within her body. He vows to cast the devil out and Sister Mary Eunice grabs him and says that she's done with him and will devour the last morsel of Mary Eunice's soul. Mary Eunice struggles for control, crying, and says that she's tired of fighting. Howard tells her to let go of him and she releases him... and he throws her over the balcony. She slams into the floor below and Mary Eunice looks up as the Dark Angel arrives. The nun asks it to take her and the Dark Angel says that she will take both of them and kisses Mary Eunice on the lips.
Later, Howard prays over Mary Eunice's corpse. Arden comes in and Howard tells him that Mary Eunice has been released from Satan's gift. Arden accuses Howard of killing her and insists that she should be cremated. Howard disagrees but Arden says that the very cells of her body were corrupted by the Devil and must be destroyed. The monsignor reluctantly agrees and offers to assist, but Arden says that he'll do it himself. Howard talks about how God sometimes sends a sign and causes a body to emit the smell of roses, but admits that he smells nothing but decay. Once he leaves, Arden wipes the lipstick from Mary Eunice's face.
Carl brings Kit to Thredson, who says that there's nothing the psychiatrist can do to reveal where he hid the tape. Thredson knows, but says that he plans to appeal to his savior complex. He opens the door and reveals Grace, holding their child. Kit wonders how she can be alive, but Thredson suggests that Arden has been up to something extraordinary in his laboratory. He slams Kit down onto the floor and Grace tells Kit that it's their child. Thredson realizes that Kit believes and says that what he does next is up to him.
A few minutes later, Thredson goes to the hydrotherapy and, following Kit's directions, removes a package from beneath a tub. To his surprise, it contains nothing but a book. Lana comes in and tells Thredson that she's the only one who knows where the tape is. She promises to find a way to send the tape to the police if Thredson hurts Kit or anyone else, turns, and walks out.
In the common room, Jude tries to remember the names of all of the patients. Sister Claudia comes in and says that Howard told her that Jude was speaking her name. Jude tells her that she wanted to say goodbye because Howard is marrying her and taking her to Rome. Rambling, Jude talks about how Howard likes her cooking and how Sister Mary Eunice raped him. Sister Claudia assumes that she's deranged and tells her to rest, but Jude points out Lana across the room. She says that she falsely imprisoned Lana there and asks Sister Claudia to get her out.
Arden goes to Briarcliff's crematorium and prepares to dispose of Mary Eunice's body. He lifts the sheet to take one last look and strokes her brow. He lies on the platform and embraces her, and then activates the mechanism and the tray slides into the furnace with both of them.