Arden manages to revive the temporarily dead Kit, who asks what happened. The doctor tells him that he almost died, just as they planned, but that he'll recover from the shock in a bit. When Kit asks if the aliens came when his life was threatened, Arden lies and says that they didn't.
A shocked Arden takes the pregnant Grace to his lab, locks the doors, and examines her. He's surprised to discover that the aliens healed the bullet wound that killed her. Pepper appears on the balcony above and tells Arden that from now on, she goes where Grace goes. Arden dismisses her as inconsequential even though she can now speak, and asks his former patient what the aliens put in Grace. Pepper refuses to answer and warns him that x-raying Grace will reveal nothing because of the aliens' protection. When Arden prepares to perform a C-section to learn more, Pepper tells him that the aliens laugh at his crude fumblings and that he's nothing like them. She telekinetically knocks the scalpel from his hand and tells him that she knows from experience that no one takes freaks seriously. If Arden does anything to harm Grace, the aliens will take him away, alter his brain, and return him as a freak. Pepper tells him to go to Mary Eunice while she takes care of Grace.
Mary Eunice takes Howard to a room and tends to the injuries on his palms and feet caused when Emerson crucified him in the chapel. She assures him that they're doing everything they can to find and capture Emerson, and that Howard is a saint for trying to see the good in the serial killer.
Howard remembers hanging on the cross and the Dark Angel coming to him. She refuses to take him, saying that God wants him to cast the Devil out of Mary Eunice. When Howard wonders how he could block his thoughts from the possessed nun, the Dark Angel tells him to focus on the rosary to protect his mind.
The monsignor clutches at his rosary and thanks Mary Eunice for her help. She all but dances off, telling him that she has new and exciting things planned for Briarcliff. Mary Eunice goes to the common room and tells everyone, including Lana and Judy, that she's put in a jukebox since Judy broke their favorite record. As she plays "I Put a Spell on You" in honor of Judy, Judy walks out. Kit arrives and goes to Lana, and the two of them talk privately. As he warns Lana that Thredson is loose, the psychiatrist enters the common room and talks to the two of them alone. He admits that he's impressed with Lana's pluck and hopes that she will pass it onto their child, well aware that the boy survived her makeshift abortion attempt. When Lana wonders if he plans to kill her, Thredson assures her that he'll need her alive to breast-feed their son for at least a year. When Kit dismisses him as insane, Thredson points out that the teenager is still a wanted man. Kit dares him to turn him in but Kit refuses, well aware that Kit has hidden the tape with his forced confession on it. When they wonder what Thredson plans to do, he tells them that Mary Eunice has hired him as Briarcliff's psychiatrist and walks away.
That night, Mary Eunice has the orderlies usher all of the female patients out of their cells for a surprise inspection. Lana takes the opportunity to grab the nun and asks what she's doing, releasing Thredson and putting him in charge. Mary Eunice tells her that Thredson will whip the asylum into shape. When Lana warns her that Thredson will eventually kill her, the nun assures her that the psychiatrist only wants what's best for Lana and the other patients. She then tells Carl to take Lana to the hydrotherapy room for a hot-water treatment.
Once Lana is taken away, Mary Eunice turns to the other patients and asks if anyone else would like to complain. Judy does and Mary Eunice goes into her cell and finds a cucumber. She accuses her former superior of using it sexually and a disgusted Judy tells her to do her worst. Mary Eunice has her taken to Arden's laboratory and tells the doctor to give Judy some electro-shock therapy. Arden eagerly agrees and prepares her, while Judy tries to get through to the real Mary Eunice trapped by the Devil. The possessed nun ignores her and says that they'll burn the bad memories out of her, and then throws the switch herself.
Later, Mary Eunice goes to Howard and treats his wounds. As they talk, he grabs her and tries to exorcise the Devil from her. Mary Eunice easily throws him off and mentally pins him to the bed. She then undresses and climbs on top of him, raping him and ignoring his pleas to stop. Mary Eunice realizes that he's a virgin and says that he should have sex at least once before he dies. Howard finally gives in and climaxes, while Mary Eunice turns and sees a shocked Arden watching from the hallway.
A dazed Judy goes to the common room and Lana and Kit watch her with the other patients. Lana admits that seeing her former tormentor tormented doesn't make her feel better. Judy goes to the jukebox and hits it, and Lana goes over and asks if she knows her name. The song "The Name Game" comes on and Judy hallucinates leading everyone in a musical number, while Lana tells her that her name is Judy Martin.
Arden goes out into the woods to throw food to his mutant experiments and Mary Eunice tags along. He's disgusted with what she did to Howard and insists that there is no longer anything between him and the nun that he once knew. Mary Eunice is eager to give Judy a transorbital lobotomy but Arden says that he won't do anything she wishes. He then shoots the mutants dead, saying that the experiment is over. Arden admits that it's a farce and prepares to shoot himself, but collapses sobbing on the ground, unable to commit suicide. When he tells Mary Eunice that she can't understand what it means to have lost her, she tells him that he's pitiful, kicks him to the ground, and walks away.
Later, Howard orders everyone out of the kitchen except Judy, who is trying to make a loaf of bread. Once they're alone, he apologizes for not believing her when she said that Mary Eunice was possessed by the Devil. Howard admits that he failed to cast the demon out and now it has stripped him of his virtue. He wonders if he should renounce his vows and asks Judy what he should do, and she tells him to kill Mary Eunice.
Thredson tells Carl to bring Kit to his office in a straitjacket and then searches Arden's office for sodium pentothal. He hears a woman's screams from the lab and goes to investigate. Pepper is there with Grace and tells Thredson that the baby is crowning.
Mary Eunice goes to Howard's room and mocks him as he prays to God for strength. He insists that they won't have sex again, but she reads his mind and realizes that he wants to kill her. The nun dares him to strangle her with his rosary like he did with Shelley, well aware of everything that he's done. Howard denies it but Mary Eunice tells him that she knows he wants power rather than sex and that together they will rise up through the Church hierarchy. Confident that Howard is too weak to resist her, Mary Eunice walks out into the hallway and Howard follows her. He taunts the Devil, saying that it couldn't even destroy Mary Eunice's purity, still trapped within her body. When Howard vows to cast the Devil out, Mary Eunice grabs him and says that she's had enough of the monsignor and will make him watch as she consumes the last of the true Mary Eunice's soul. Mary Eunice manages to fight free, crying, and says that she's tired of fighting the Devil. Howard tells her to let go and she does... and he throws her over the balcony. She falls three stories to the floor below and lies dying. The Dark Angel appears to her and says that it will take them both, and kisses Mary Eunice on the lips.
Later, Howard prays over Mary Eunice's corpse as Arden comes in. The monsignor tells him that the nun is finally free and Howard insists that they cremate the body since its cells were corrupted by the Devil. Howard reluctantly agrees and offers to assist, but Arden says that he'll handle it himself. As the monsignor starts to leave, he tells Arden about how sometimes God will cause a corpse to give off the scent of roses as a sign, but admits that he smells nothing but decay.
Once Thredson has Kit in his office, he explains that he knows Kit would die rather than reveal where the tape is hidden. However, the psychiatrist plans to play to Kit's savior complex and leads him into the next room. Grace is there with her child while Pepper looks on, and Thredson tells a shocked Kit that Arden must have done something to bring Grace back from the dead. Grace tells Kit that the baby is their child and Thredson says that what happens to it next is up to Kit.
A few minutes later, Thredson follows Kit's directions and goes to the hydrotherapy room to find the hidden tape. He's surprised to discover that it's been replaced with a child's book. Lana comes in behind him and informs him that she is now the only one who knows where the tape is. If Thredson hurts anyone, she promises to get it to the police.
In the common room, the dazed Judy tries to remember her name but can't. Sister Claudia visits her and says that she came in response to Howard's summons. Judy rants about marrying Howard and going to Rome with him, and how Mary Eunice raped the monsignor. Sister Claudia tries to get through to her but Judy points out Lana and admits that she is falsely imprisoned, and asks the mother superior to get the reporter out of Briarcliff.
Arden takes Mary Eunice's corpse to the crematorium and places her on the delivery tray. After stroking her brow, he lies on the platform with her, activates the mechanism, and slides into the furnace with the dead nun.