Johnny Morgan is at home and calls a prostitute, Pandora. She assures him that she's brand-new after giving birth three weeks ago. Once she gets her money, Johnny confirms that she knows what he wants from his description. Pandora assures him that she has stopped breast-feeding and is ready for Johnny. They talk about how she lactates when she hears a baby crying and Pandora removes her blouse. She asks how badly Johnny wants it and he says that he'd kill for it.
Thredson goes to see Kit in his cell and assures him that his baby son is doing fine. The psychiatrist prepares to reunite father and son and Kit asks what Thredson's end-game is. Thredson tells him that he has a great respect for children and that they are both alike because they'd both do anything for their own children. They go to the common room where Pepper is standing guard over Grace and her child. Grace tells Kit that she's named the child Thomas after her grandfather and Kit happily agrees. Thredson tells the new mother that he'll be glad to help with her lactation problems and that he knows how important breast-feeding a child can be. Pepper warns him off and Thredson has Carl take her to the hydrotherapy room.
Once Thredson leaves the couple alone, Kit holds his son and asks Grace what happens. She explains that she's had vague memories that she can't entirely piece together. She describes how after she was shot, she entered a bright white light. The aliens then placed their son into her womb and that the child grew faster because time didn't pass at the same rate. Kit asks about Alma and Grace admits that her abductors weren't perfect and that they lost Alma. Kit wonders why the aliens wanted Alma and Grace, and Grace explains that Kit is the special one and that they're linked to him. She explains that Thomas is special as well and has a destiny as someone who will change the way that people think. Kit figures that Alma would want him to do the right thing and proposes to Grace on the spot, and she agrees.
Before the couple can celebrate further, Howard comes in with a Sister Colette from the local Catholic orphanage. The monsignor tells them that he will be turning Thomas over to the orphanage because a sanitarium isn't the place to raise a child and because both of Thomas' parents are convicted criminals. Colette takes the child away while the orderlies restrain Kit and Grace. Thredson returns and tells Kit that he understands his heartache, and offers to help.
In the kitchen, Sister Claudia finds Lana and talks to her privately. The mother superior tells Lana that she's helping her escape on behalf of Jude, who told her what she did to Lana to imprison her at Briarcliff. When Lana wonders how she will prove what happened there, Claudia gives Lana her patient file which documents everything that was done to her. Lana realizes that Claudia wants Briarcliff destroyed as much as she does, and Claudia tells her that a taxi will be arriving soon and they don't have much time. Before she goes, Lana takes Thredson's confession tape out of a drawer. The reporter says that she has one last thing to do and then goes to the common room and tells the dazed Judy that she will come back and get her out.
Thredson talks to Kit in the lobby and tells him that he will reunite Kit with his wife and child if he gets the confession tape for him. Lana, walking by, walks behind them out of the lobby. Meanwhile, Thredson tells Kit that he'll frame Arden for the Bloody Face murders so that he can get Kit released. Kit warns Thredson that Lana won't tell him and the psychiatrist suggests that he be very persuasive. Realizing something is wrong, Thredson goes outside and sees Lana get into the waiting taxi. She holds up the confession tape in triumph and gives Thredson the finger as the driver leaves.
That night, Thredson returns to his apartment and finds an armed Lana waiting for him. She tells him that she gave the tape to the police and there'll be there soon, but she wanted to be there first because Wendy is still missing. Thredson smiles and admits that he's relieved and makes himself a drink. As he opens the drawer, Lana is unaware that there's a gun in the drawer. The psychiatrist explains that he's going to have one last martini and Lana reminds him that he was the one who chained her to a bed and called her Mommy.
Johnny finishes suckling as Pandora tell him to call her Mommy. He admits that he has a fixation on his mother, who never loved him or his father.
Lana demands to know where Wendy's body is hidden so that she can give her lover a decent burial. Thredson turns on the fireplace and explains that Wendy was the first victim he took that was still intact when he finished. He decided to keep her corpse for practice and made love to it. Once he turned her around and took the corpse from behind, he was able to climax and overcome his impotency issues... allowing him to rape Lana. After Thredson finished, he cut up Wendy's body, burned what he could, and scattered the remaining pieces around the countryside.
Pandora embraces Johnny as he breaks into tears. After a moment, he shoves her away and complains that his mother is the one making him upset. He starts smashing furniture and Pandora begs him to help provide some relief. Furious, Johnny goes over and starts strangling her.
The police arrive and Thredson goes to the bar for a second martini. Lana tells him to drink up and Thredson realizes that Lana will never let their child live. When Lana says that he wouldn't have the chance even if she did keep the child because he'll be executed, Thredson boasts that he's insane. He figures that he will be sent to Briarcliff and live out his life. Thredson informs Lana that he no longer has a use for her and starts to reach for the gun, and Lana shoots him in the head.
Sometime later, Lana and her friends Barb and Lois go to the mausoleum to see Wendy's coffin. As Lana places flowers, she admits that they never did find Wendy's body but that she needed someplace where she could remember her lover. The reporter tells her friends that she plans to move to New York once she cleans up her old house. Barbara confirms that Lana has the address of a doctor who can help her. Two reporters sneak in and take pictures of Lana, and she tells her friends that they'd better sneak out the back so that they aren't associated with the "Sapphic Reporter" that the newspapers are pushing her as. Lois and Barbara hold hands, apologize for abandoning Lana rather than stand with her, and leave out the back. Lana then goes out the front and gets into a car. The reporters have gathered around and shout questions, but all Lana will tell them is to read her book.
At Briarcliff, Judy is getting her daily medicine but finally snaps and throws away one patient's pills. She says that they're nothing but horse tranquilizers, and the nuns reminds her that Judy was the one who ordered them. Furious, Judy slaps the tray of medicine away from them.
Howard is in his office reading all of the newspaper articles about Bloody Face and the atrocities at Briarcliff. He calls in Father James, who tells the monsignor that the reporters have been escorted out but are camped out in front of the asylum. Howard figures that things will blow over if he refuses to give a statement, and James tells him that Judy is causing a commotion. Howard goes to see her and finds her listening to the new jukebox. He sits down with her and asks what she wants, and she points out that he lost his virtue to the Devil. When Judy asks if he will renounce his vows, Howard says that he still has too much to do. Judy admits that she had impure thoughts about the monsignor and would have done anything for him, but now she is disgusted by his ambition. Howard grabs her and says that she's an embarrassment to him, but Judy tell him that she's more sane now that she's been committed than she ever was when she ran the place. As Howard has Carl take Judy to solitary, Judy warns him that God won't let him prevail.
Later, Kit is in his cell when Carl brings him a package of donated clothes and a clipboard with release papers. The orderly explains that Kit is being released because Lana killed Thredson and the reporters are snooping around Briarcliff. They want Kit to leave to cover up what happened to him. Kit signs the papers but then asks to see Howard. When he's escorted to the monsignor's office, Kit demands that they return Thomas to him. Howard points out that Grace is still a patient and a convicted axe murdered, but Kit threatens to go to the reporters if he doesn't get what he wants. The monsignor wonders how he can possibly release Grace given her history, but Kit points out that Arden already filed an official death certificate for Grace and Frank signed it before he died. As far as anyone knows, Grace is dead.
Howard gives in and Grace and Kit return to Kit's home. They go in and Kit admits that he hasn't had a chance to clean up the place since the aliens abducted him. Grace is simply relieved that she isn't in Briarcliff anymore. As they kiss, they hear someone in the kitchen. Kit goes in to investigate and finds Alma seated at the table... holding a baby.
Lana meets the abortion doctor at a motel and explains that Thredson raped her and killed he lesbian lover. As the doctor begins the procedure, Lana remembers everything that happened to her and all of the death that she saw. She stops the doctor and says that she can't face another death.
Several months later, a visibly pregnant Lana goes to the police station and shows detectives Byers and Connors her patient files. She also has the files on all of the patients that disappeared, but the detectives admit that they don't have any other evidence. The Church has transferred Claudia to Puerto Rico and Lana wants the detectives to get her into Briarcliff so she can have Judy verify her story. Byers asks if Bloody Face is the child's father and Lana tells him that the baby doesn't have a father.
The detectives get a court order and take Lana to Briarcliff. They go to Howard's office but the monsignor tells them that Judy hung herself in her cell. He has the death certificate and explains that they cremated the body because Judy died outside of a state of grace. When Lana accuses him of killing Judy, Howard tells her that he only wanted good for Judy and blames Lana, pointing out that if she had come a few weeks earlier, Judy might still be alive.
Once Lana leaves, the orderlies deliver food to the patients. The last patient isâ€¦ Judy, locked up in solitary and praying to St. Jude for a miracle.
Several months later, Lana gives birth and tells the staff to keep the child away from her. However, a neo-natal nurse brings the baby in anyway and explains that the child is allergic to formula. She had hoped that Lana breast-feeding the boy might keep it quiet, and Lana reluctantly takes it. As she breast-feeds it, it calms down and Lana looks at the crucifix on the wall in quiet despair.