Sister Jude drives into town and meets with Sam Goodman. He assures her that confidentiality is important to his work and Sister Jude assures him that the mother superior, Sister Claudia, is the only one that knows she is there. Sam assures her that what he does is a calling and she asks if he lost someone. In response, the man reveals the concentration camp tattoo on his arm and says that he lost everyone. Sister Jude gives him the file that she has on Arden and explains that he may have been a SS doctor, Gruber. After reviewing what little there is, Sam explains that after the war, the intelligence agencies recruited the best Nazi scientists and created false biographies to get around Truman's orders. He asks if Sister Jude has seen Arden without his shirt on. When she says she hasn't, Sam explains that SS officers have a tattoo of their blood type on their arm. He tells Sister Jude not to do anything for fear it might alert him.
At Briarcliff, Sister Mary Eunice is going through Sister Jude's desk when Anne Frank brings the wounded Arden in. Arden tells Sister Mary Eunice to go and she leaves, and Frank the guard comes up behind Anne and holds a gun to her head, telling her to surrender.
Anne wakes up later and finds herself in a straitjacket in a cell. Sister Jude comes in and asks her where she got the gun, and Anne explains that she took it from one of the detectives. She insists that Arden had a monstrosity in his lab and got rid of it, but Sister Jude points out that he was in no condition to get rid of anything. The nun tells Anne to focus, warning that Arden will soon be back from the hospital and may take Anne to his operating table. Anne tells her to look in Arden's lab and the nun says that she and Frank went there and found no sign of the creature Anne described.
Sister Mary Eunice comes in and interrupts, telling Sister Jude that Anne's husband Jim Brown has arrived. He explains that "Anne" is Charlotte Brown, born Charlotte Cohen. Their son David has the colic and his constant crying strained the high-strung Charlotte. Sister Jude admits that she was a convincing actress and Jim says that Charlotte read the book and saw a production, and then put the tattoo on her arm. It started when they had David and Charlotte started talking about the babies who were gassed and tortured. Eventually Charlotte said that there were other babies who needed her and would work on her project studying concentration camps.
Thredson has been listening in and suggests post-partum depression. Jim insists that Charlotte is simply emotional and needs to come home, but Thredson warns against it. Sister Jude sides with Jim and she has the orderlies give Charlotte a dress and bring her down. Jim greets her as Charlotte but she insists that her name is Anne. When he tries to take her hand, Charlotte insists that she's a death camp survivor and Jim has no idea what she is. Sister Jude tells her to go home and Jim shows Charlotte a photo of the family. She looks at it, insisting that it can't be, and Jim says that he and the baby need her. As he leads her away, Thredson watches and warns Sister Jude that she's making a mistake. He asks her about the rumor that she's ordered Kit's medical sterilization and Sister Jude tells her that it's no rumors. Thredson warns that it's illegal but Sister Jude ignores him and walks away.
In his cell, Kit calls to Grace and asks if she's afraid. She says she isn't but he doesn't believe her. Kit remembers Alma saying that they would have children but now neither he nor Grace will have any. He apologizes for getting them into the mess but Grace says that the only one to blame is Sister Jude. Sister Mary Eunice and an orderly arrive and she tells Kit that Sister Jude changed her mind because he showed signs of redemption. He asks about Grace and Sister Mary Eunice assures him that she hasn't forgotten about her. Once Kit is led away, the nun tells Grace that she will go under the knife in the morning.
Time passes and an unearthly light shines behind the door to Grace's cell. She stares into the light as something enters the room.
Lana gets her medication in the common room and stares out the window. Thredson approaches her and says that they're leaving after dinner, and the reporter wonders if it's real. He tells her not to be late and then goes to see Kit. Kit begs him to help Grace but Thredson says that she's not his patient and promises to do what he can once they finish with Kit. The psychiatrist begins recording and says that Kit should confess to killing the three women, but only if he believes it's true. He's going to record Kit describe what happened and then play it back to him so that he can hear and accept what he's done. They begin and Kit says that he murdered his wife.
Grace sees Alma standing over her, telling her not to fight it. Aliens then begin dissecting Grace.
Sister Jude calls and leaves a message for Sam saying that the information was wrong. Arden comes in and overhears her, and asks what information she's talking about. He invites her to tell him and then asks what she saw in his lab. Sister Jude says that she was simply following up on a patient complaint and she found nothing interesting. Arden says that he's pressing charges against Sister Jude for letting Anne get ahold of a gun and then sending her home without punishment. The nun says that she hopes they can start afresh but Arden tells her to grovel. When Sister Jude refuses, Arden says that he'll call Monsignor Howard and demand her dismissal
Arden returns to his office and removes his pants to check on his leg wound. Sister Mary Eunice comes in, assures him that she's had training as a nurse, and tends to his wound. She apologizes for her behavior on the night of the storm and he says that they'll never speak of it again. Arden thanks her for protecting him and Sister Mary Eunice says that she protected them by disposing of Shelley. She's glad to help him continue her work and suggests that she can help him once Howard puts him in charge.
At the school in town, the children go out for recess and one girl, Peggy Cartwright, hears moaning noises from the stairs leading to the basement. She sees Shelley and goes to get the teacher. When they come back, they see Shelley crawling up the stairs toward them and run screaming in terror.
Charlotte is brought back to Briarcliff and Sister Jude takes Jim to her office. Arden watches her taken to her cell and goes to see her. Meanwhile, Jim says that he has to go to work and he can't trust Charlotte alone with the baby. When he took Charlotte home, she grew worse as the baby kept crying. Finally she tried to smother the child and Jim shoved her away. He begs Sister Jude to take her and suggests that Thredson might look after Charlotte. Sister Jude invites him to consult with Thredson if he wants and has Frank go to bring the psychiatrist there.
Thredson meets Lana beneath the stairs, puts a coat over her shoulders, and tells her to walk out with him past the guard. They walk past and the guard, Jimmy doesn't notice. However, Frank comes down the stairs and calls to Thredson.
Jim goes to Charlotte's cell as Arden emerges. The husband thanks Arden for not pressing charges and Arden says that he sees no reason for punitive action. Arden suggests a more humane approach and says that they can do it that night and then Charlotte will be a new woman.
As Thredson gets Lana out to the car, Frank follows him out and says that Jim wants to see him. Thredson says that he doesn't work there anymore and never did. As Frank goes back inside, Thredson gets in the car and drives off with Lana.
Arden has Charlotte brought to his lab and prepares for a lobotomy. When Jim wonders if it's safe, Arden assures that it's a simple and routine procedure in his hands.
Sister Jude is praying in her room when Frank comes in and tells her that Lana has escaped. She talks about how she came home from school to an empty house and brought in a baby squirrel for company. One day she came home and discovered that it had died because she had forgotten to feed it. Jude put him on the table and prayed for several hours. Her mother came home, screamed, and threw the dead squirrel in the garbage. Sister Jude laments how God didn't answer her prayers and that her mother told her that God never answers prayers the way someone is looking for. She admits that she's done at Briarcliff and Frank offers her condolences, saying that as a woman she never had a chance.
Arden administers anesthetic to Charlotte and then performs the lobotomy.
Sister Jude puts on a dress and goes to a local bar. She lights a cigarette and a man comes up and offers her a drink.
Thredson takes Lana to his apartment and she says she wants to go to her home. He points out that they'll search there first for her and that he has set up a meeting with a Detective Spears in the morning. Thredson offers her a glass of wine and goes to the kitchen to get it. Lana looks around and finds a phone. She dials her friend Lois to ask about Wendy but Thredson comes out and hangs up the phone. He reminds her that he's at risk for breaking her out and that they can't afford to go public until the next morning.
As Lana sits down, Thredson tells Lana that she'll win a Pulitzer for telling his story. She wonders what he means and then offers a toast to taking down Briarcliff. He joins in the toast and turns on the lamp, and she notices that the lampshade is made of human flesh. Thredson offers her mints from a bowl that appears to be made from part of a human skull. Lana asks to use his restroom and Thredson gives her directions.
Once she's out of sight, Lana tries the doors and discovers that all of them are locked except one. She goes in and finds a workshop filled with cutting tools. Thredson comes in and explains that he makes lamps using human skin. He then pushes a button and a trapdoor opens beneath Lana, dumping her into the basement.
Kit goes to the common room and finds Grace sitting in a chair. She is bleeding from the groin and Kit realizes that Thredson broke his words. Detectives Byers and Connors come in and place Kit under arrest for the murder of the three women. He tells them to talk to Thredson but they say they have the psychiatrist's report and Kit's taped confession. As they take him away, Grace screams that she saw Alma alive, but the detectives ignore her and haul Kit away.
Lana wakes up and finds herself in a tiled room with more tools. Thredson has chained her to the floor and left. Lana calls but gets no answer, and sees Wendy lying on the floor nearby. She reaches for her and discovers that her lover is dead and covered in ice. Thredson comes in and explains that he had hoped to keep her fresh. He explains that normally he removes the skin and head by now but he kept her around for a little longer for his purposes. Thredson then tells Lana that they are going to continue their therapy and tells the reporter to kiss Wendy's corpse. He dons a Bloody Face mask and points out where he's attached Wendy's teeth.
Jude wakes up next to the man from the bar. She dresses and leaves before he wakes up.
Jim comes home and greets his wife and child in Charlotte's study. A smiling Charlotte holds her son and assures Jim that she has made a pot roast and will get him a drink. He notices a box filled with her World War II files and she tells him that it's trash. Jim offers to take it out and asks if Charlotte is happy, and she assures him that she has never been happier. As they leave, a few photos are still on the boards... including one of Arden standing behind Adolph Hitler.