At a homeless shelter, Reverend Daniel Beeson sends his assistant home and starts cleaning up. A homeless man, Daryl, knocks on the door and asks for an extra coat. Daniel lets him in to find a coat. Once Daryl is gone, Daniel goes to his apartment and smokes and drinks. He hears a pounding at the door again and goes to answer it: Jesus is at the door, bleeding and levitating.
House arrives and Cuddy asks him to come for Rachel's baby-naming ceremony. He considers the whole thing hypocritical but Cuddy insists that he come. House says he'll think about it and goes to the ER to mock Cameron, who is back at her normal job. House goes through the files for his next patient, Daniel. Cameron dismisses Daniel's Jesus sighting as a drunken hallucination. House notes she isn't sure what brought on the hallucination and summons the team for a differential. They figure House either wants to screw with them or Daniel. House concedes it could be either or both and sends them out to test Daniel and the shelter. Before they go, House tells Thirteen and Foreman to choose between their relationship or their job: one of them has to quit once the current case is resolved.
Kutner and Taub test Daniel and note that he traveled several times. Daniel explains that he was accused of child molestation and was transferred repeatedly, but insists it isn't medically relevant. He denies molesting the child, but Taub suggests that syphilis might account for the hallucination. Daniel says he hasn't had sex and notes that he doesn't really think he saw Jesus either.
House and Wilson have lunch and Wilson admits he's going to Cuddy's christening ceremony. House would rather Wilson avoid the whole thing and Wilson wonders why Cuddy invited him. House admits that it's flattering.
Foreman and Thirteen discusses House's ultimatum and she wonders why Foreman insists on working with House. Foreman finally admits she's right and he's going to stop House from putting them through his most recent game. He says they're not going to do anything.
House doesn't think that Daniel is innocent of the molestation and Taub agrees, but Kutner isn't so sure. Taub doesn't think there's anything wrong with Daniel and House agrees. Foreman and Thirteen tell him neither one of them is quitting, and House tells Foreman he's fired.
Taub and Kutner prepare to discharge Daniel, who says that his foot is numb and he feels nauseous. Taub wonders why he's so intent on staying but Daniel insists he's ill. Kutner examines the foot and discovers that his toe fell off due to necrosis.
House is happy they've got a real case, and Kutner and Taub wonder where Foreman and Thirteen are. House explains Foreman quit and Thirteen is taking a stand for the moment. House tells Taub and Kutner to check out Daniel's house and put the priest in a hyperbaric chamber in case of carbon monoxide poisoning.
As Foreman packs, Thirteen wonders what they're going to do. He admits that their relationship would affect his judgment. Foreman insists she shouldn't quit and they'll both be fine. As they kiss, Thirteen gets a page to check on Daniel.
At the shelter, Kutner and Taub discuss Foreman and Thirteen's relationship while going over Daniel's apartment. Meanwhile, House and Cuddy are in the elevator and House insists she's a hypocrite. Cuddy insists it's a sincere invitation and she wants him to come, and he says he'll be there. Cuddy then goes to Wilson and blames him for convincing House to come to the christening when she only asked him to cover her bases. She tells Wilson to fix it and make sure House doesn't figure she told Wilson to do it.
Daniel's necrosis stabilizes but he starts to panic in the hyperbaric chamber. They get him out of the chamber as he appears to have a heart attack.
Foreman goes to see Cuddy for a letter of recommendation. She points out that House is right and refuses to give a recommendation.
Back in differential, the team rules out a heart attack and House suspects it's a clotting disorder. He orders them to do an angio and Thirteen hesitates, and House goes to see Daniel. The priest insists everything he's said is true and God has forsaken him. House is impressed with his attitude. The angio shows negative but Daniel says that he's not feeling any pain from the probes to the chest. House believes it's neurological and orders testing to confirm.
Wilson asks why House is going to Cuddy's ceremony, and House says he's fulfilled his obligation to Cuddy. He figures Cuddy is trying to play him and he refuses to let her get away with it.
Thirteen approaches Cameron about getting a job in the ER. Chase tells her not to quit but warns against office romances. He and Cameron wonder if Thirteen needs to stand up to House, or if House is actually doing them a favor because he thinks their relationship won't work out. Cameron offers to make a call for her.
As Taub and Kutner conduct the tests, Kutner asks Daniel about his faith but the priest doesn't believe it. They find intercostals neuralgia, trauma to a nerve in the rib. Daniel tells them that his right eye has gone blind.
The team goes back into differential and Thirteen returns. They're unable to find any structurally damage to the eye but his body is shutting down. Thirteen suggests autoimmune, cancer, and infection, but the tests prove negative. House figures that Daniel has an infection but his spleen is failing so there are no white cells to indicate infection. He orders Taub and Kutner to do a biopsy, and once they're gone Thirteen asks House if he'll hire Foreman back if she quits. She claims Foreman is okay with the plan and House agrees.
House goes to see Daniel as they conduct the biopsy. They discuss Daniel's loss of faith and House wonders if Daniel is hoping to get it back. Daniel says he has nowhere else to go, and challenges House's own hypocrisy: he treats people even though he claims not to care about them. The priest figures House is looking for someone to give him hope. House dismisses his theory and leaves, where he runs into Cuddy. She tells him she doesn't want him there and House quickly agrees not to come. Cuddy is surprised he gave in but ends up thanking him for not coming.
As Taub and Kutner run the tests, they advise Thirteen on whether she should stay or go. Kutner thinks they should stay together, Taub thinks they should break up. The spleen tests show some bugs.
House discusses faith with Daniel, who figures that House has a thing for Cuddy. Taub arrives to tell House in private that Daniel has pneumocystis, which is harmless unless Daniel's system is compromised: by AIDS. Daniel insists he doesn't have AIDS but refuses to let them test. The treatment could cause serious internal damage but Taub insists they go ahead and also test the boy that Daniel is accused of molesting. They can't violate doctor confidentiality by informing the boy's parents and House orders them to treat Daniel for AIDS.
At home, Thirteen tells Foreman she's found a job and tells him House has agreed to hire Foreman back if she quits. Foreman insists he wanted to handle it and gets mad at Thirteen for giving in to House.
As they eat, Wilson wonders why House is so obsessed with Cuddy being a hypocrite. He figures House is being a hypocrite and he really wants to go. House denies any interest in going.
Taub secretly goes to see the boy that Daniel is accused of molesting, Ryan, and suggests he should get tested. Ryan seems curiously disinterested in himself but asks how Daniel is doing. While he says he's been tested, he refuses to tell Taub the results.
Foreman goes to House and demands his job back. Thirteen realizes something is going on and wonders why Foreman didn't tell her he was going to get her fired by going back to work for House. House watches as the two of them argue until Thirteen storms out. House tells Foreman he can either patch things up with Thirteen or get his job back. Foreman chooses the job.
As Kutner administers the anti-AIDS treatment, Daniel's chest breaks out in a rash. Taub thinks it's a reaction to the treatment but House suggests that it's hyper-IgE syndrome. The IgE levels are normal and Thirteen suggests genetic micro-tumors. Foreman disagrees and they argue. House tells them to run the genetic tests on Daniel. As Taub and Kutner run the tests, Ryan arrives and apologizes to Daniel.
Wilson tries to convince House to overlook Cuddy's hypocrisy so he'll go to the christening. Wilson talks about how even if an absolute truth exists, they can't know all of it so House can't condemn her for failing to do so. House gets an idea and starts reviewing the symptoms on the board. He finally eliminates the hallucination, saying it isn't a symptom. He goes to Daniel's room and tells him he has Wiskott-Aldrich Syndrome. It's similar to AIDS and impairs the immune system. It's genetic and can be confirmed with a test. House claims that the hallucination was brought on by drinking and was just a coincidence. Daniel notes that the coincidence brought him to House, who cured him, and wonders how his life could improve in a single day. House tells him that everything that happened can be rationally explained, but Daniel notes it's a lot of coincidences.
Cuddy visits Cameron and they note that House managed to succeed again even though he violated his own principles. Cameron figures Cuddy wants House at the ceremony, and tells her to tell House how she feels. As House leaves, Cuddy approaches him and they make small talk. They go out and leave in separate directions.
Cameron, Chase, and Wilson attend the christening.
Thirteen returns to Foreman's apartment and they kiss.
House sits in his apartment and plays a serenade on the piano… alone.