A young priest, Fr. Daniel Bresson, runs a homeless shelter. After he gives a man a sweater to keep warm, he breaks out some liquor and begins to drink at a dangerous rate. He hears a knock at his door and opens it, horrified to find an apparition of a bleeding Jesus Christ hovering a foot off the ground. Fr. Bresson passes out and is taken to Princeton-Plainsboro. House takes the case from Cameron, who tells him there is nothing to diagnose, as Fr. Bresson simply drank too much bourbon. House seems to realize this, but takes the case as a diversion for Kutner and Taub while he confronts Foreman and Thirteen about their relationship. While the team test Bresson's EEG for epilepsy, House calls Foreman and Thirteen in. He gives them the option to "split or quit," as he feels their relationship is clouding their judgment as doctors and diagnosticians. He tells them they have until the end of the case to decide.

In the lobby of the hospital, Cuddy asks House to come to her baby daughter Rachel's simchat bat, a Jewish baby-naming ceremony.

While performing Bresson's EEG, Taub and Kutner learn more about him. Taub, intrigued by Bresson's seemingly constant job relocation, asks him for an explanation. Bresson admits to having an alleged inappropriate relationship with a teenage boy a few years back; once that is exposed, no church would keep him. Kutner and Taub report this to House, who declares the case is over. Then at lunch, House and Wilson talk over Cuddy's invitation, and Wilson tries to convince House to go.

Foreman and Thirteen, after discussing their options over lunch, decide to "do nothing." Foreman says that House is just pulling them around as an incentive to work harder. Unfortunately, when they report their decision to stay put, House immediately fires Foreman, who reluctantly hands over his hospital ID card and leaves. When Taub and Kutner report to Bresson he is being discharged, he pleads to stay, saying he knows something is wrong. Kutner looks under the sheet and finds a black toe in Bresson's bed, which fell completely off his foot. House suspects carbon monoxide poisoning, and orders them to put the priest in a hyperbaric chamber. Cuddy again asks House to come to the ceremony, and this time he immediately agrees. Annoyed, she goes to Wilson and asks him to uninvite House, saying she doesn't want him there and that Wilson prodded him to go.

Meanwhile, Bresson suffers what appears to be a heart attack in the hyperbaric chamber. Foreman goes to Cuddy and asks for a letter of recommendation, but she tells him she can't give it to him because his breach of protocol during the drug trial put the hospital and Cuddy's reputations in jeopardy. Foreman sighs but nods his understanding. Later, House debates Bresson on God and faith while testing his lungs. Kutner apologizes for the pain as he pulls the catheter out, but Bresson says he didn't feel any pain. House discovers a new symptom: regional anesthesia. House orders a nerve conduction study.

Taub and Kutner perform the study on Bresson, and they end up finding an intercostal neuralgia affecting a nerve that runs along the ribs. Suddenly, Bresson's right eye loses sight, even though nothing is structurally wrong with his eye. With his heart rate down, sensory loss and progressive muscle weakness, the patient is shutting down. House uses a metaphor of a rock band and its lack of fans to illustrate the absence of white blood cells, concluding it must be the spleen. As Taub and Kutner perform a biopsy, they discover that Bresson has pneumocystis, a parasite that he contracted through the church holy water. Pneumocystis is virtually harmless, except to people with compromised immune systems. From this, House concludes that Bresson has AIDS. Bresson, shocked, tells the team not to test him for AIDS, as he doesn't believe it is true.

Thirteen decides to quit in exchange for House offering Foreman his job back, since he can't find one. Foreman disagrees, thinking he can handle it himself. Thirteen gets angry. Foreman goes to House to ask for his job back behind Thirteen's back. They argue in front of House. Thirteen storms out. House offers Foreman a decision between Thirteen or his job. He chooses his job. Taub goes to find the boy that Bresson allegedly molested to tell him he should get treated for AIDS. The boy, Ryan, is at first indifferent, but later comes to visit Bresson and cries by his bedside, asking for forgiveness for his lying. Bresson puts his hand on Ryan's head and forgives him.

House and Wilson argue about Cuddy until House has a realization. As Wilson protests, he erases "hallucination" as a symptom on his whiteboard and concludes that Bresson has Wiskott-Aldrich syndrome, a genetic condition whose symptoms mimic those of AIDS.

Cuddy tells Cameron the news about the patient. Cameron then suggests that Cuddy invite House to the ceremony again. Cuddy sees him in the lobby but neither can make a move, and House leaves. (The camera now begins alternating between scenes as music plays through the end of the episode.) House sits in his apartment alone, drinking and playing the piano. Foreman is sitting reading the paper when Thirteen walks in and smiles, taking a staged "Broadway-esque" bow, hinting at the fact she and Foreman just played House. She and Foreman kiss. Meanwhile, the ceremony is taking place at Cuddy's house. House gazes for a few seconds, in contemplation, but never goes to Cuddy's, instead going back to playing piano, while it shows Cuddy's party. When the doorbell rings, Cuddy hands Rachel to Cameron, but when she finds other guests at the doorstep, she greets them warmly but with a look of slight disappointment that they weren't House.