A gunfight ensues in a makeshift graveyard, as actor Garry Shandling, dressed in the requisite FBI suit, checks the clip on his gun and clutches at a pottery bowl under his arm. A priest in the flowing robes of a Catholic Cardinal holds red-wigged actress Tea Leoni at gunpoint. This "Cigarette-Smoking Pontiff" addresses Shandling as "Mulder," offering to trade "Scully" for the bowl. Shandling warns the CSP that if the Lazarus Bowl is smashed, then all the sniper zombies that the CSP has ready to attack will revert back to being corpses. A zombie steps forward to plead with Shandling: "C'mon man, don't break the bowl. We don't wanna go back to being dead -- no food, no women, no dancing." The zombie offers to make Shandling the king of the dead, but Shandling refuses, stating that he'd "rather serve in heaven than rule in hell." And with that nod to Milton, he throws the Lazarus Bowl high in the air to allow Leoni to disarm the CSP. As Shandling leaps toward her, a zombie dives for the falling bowl. Shandling and Leoni tumble down the hill and fall into an open casket. Lying on top of "Scully," "Mulder" professes his love after seven years of waiting and passionately kisses her.

The graveyard scene, it is revealed, is really only a movie. The well-dressed audience watching the film includes Shandling and Leoni, as well as the real Scully, who stares up at the screen with wide-mouthed disbelief. Next to her is the real Mulder, his head held low in abject humiliation. He looks across the aisle to Skinner, who is beaming from ear to ear. Skinner raises his hands and shrugs innocently at Mulder.

Eighteen months earlier: Skinner briefs Mulder and Scully in his office about a bombing in the crypt of a D.C. church. Wayne Federman, a screenwriter and college friend of Skinner's, listens to the conversation, but his ringing cell phone and commentary into a tape recorder disrupts the meeting. Skinner instructs the agents to allow Federman to tail their investigation for research on his latest script. With Federman on his heels in the crypt of the church, Mulder questions Cardinal O'Fallon about the incident. The crypt contained only relics and documents, but nothing of any monetary value. Suddenly a cell phone rings, and Mulder immediately looks disapprovingly to Federman. The ringing, however, is coming from a phone held by a body beneath the rubble. Mulder identifies the corpse as one of his idols, Micah Hoffman, a counterculture revolutionary from the 1960's.

Federman follows Mulder and Scully to Hoffman's apartment, where they find not only bomb-making materials, but forging instruments and fake religious documents describing an account of Christ's life on earth after his resurrection. As they return to the crypt, Federman tells Mulder that he admires the agents' underhanded way of working. "No warrants, no permission, no research -- you're like studio executives with guns," he says. While Mulder discovers remnants of Hoffman's forgeries, Federman watches in astonishment as human bones animatedly try to reassemble broken pottery. He recounts the scene over breakfast at a diner, and Scully acknowledges that he must have been hallucinating the events. Yet Federman, filled with enough "flavor" for his movie, decides he's had enough and leaves. Scully admits that his story reminded her of an old Catholic school tale about the story of Jesus raising Lazarus from the dead. His incantations were engraved on a bowl being spun on a wheel nearby, like the grooves on a record. Mulder is intrigued by this idea, and sends Scully to consult with their expert friend Chuck Burks. Chuck analyzes the bowl and finds that all the notes vibrate in exactly the same key -- a feat unheard of in music.

Meanwhile, the Cardinal despondently tells Mulder that he purchased the forgeries from Hoffman and intended to hide them because he believed they were real. The Cardinal had hoped to protect others from the despair and anger he felt when he read the documents. Mulder phones Scully to ask her to do Hoffman's autopsy, suspecting that the Cardinal may have murdered Hoffman for blackmail over the forged papers. Federman beeps into Mulder's phone and invites him to Hollywood to watch the filming of the movie based on their X-file. Mulder is somewhat flattered, but his interest is tempered when he learns that while Tea Leoni and Richard Gere have been cast to play Scully and Skinner, Garry Shandling will play Mulder.

In the autopsy bay, Scully dissects Hoffman's heart when, suddenly, the corpse sits up. "I'm gonna need that when you're done with it," Hoffman says as he hops off the gurney and gives himself a shake. Scully gapes, reaching out to touch him with her scalpel. Hoffman warns her off and she drops the scalpel. She reaches for it and looks up again, but the body is back on the table. She brushes off her hallucination to fatigue. Mulder arrives later and Scully informs him that Hoffman's stomach was filled with red wine and strychnine. Mulder theorizes that the Cardinal must have poisoned him with Communion wine. Cardinal O'Fallon is conducting Mass when Mulder and Scully arrive with an arrest warrant. Scully asks her partner to allow the Cardinal his dignity and the two wait. She goes to kneel before a crucifix and sees Micah Hoffman on the cross. He looks directly at Scully and says "Consummatum est." When she turns around, the crucifix is back to normal. Disturbed, she leads Mulder to arrest the Cardinal. As Mulder reads the Miranda Rights, a man walks into the church. It is Micah Hoffman, very much alive.

Skinner angrily censures the agents for misidentification of a corpse and false arrest, while Mulder and Scully seem scared to meet his gaze. Skinner forces them to take four weeks' probationary leave while their actions are investigated. They head back to their office to find Chuck Burks waiting. The clay bowl's vibrations rendered into actual words in ancient Aramaic, the language that Christ spoke. He says that the first part roughly translates into "I am the walrus, I am the walrus, Paul is dead, coocoocachoo." The second part seems to be one man commanding another to rise from the dead. Mulder and Scully decide to visit Hoffman, who announces that he has become Jesus Christ. Off their skeptical expressions, he explains that in order to forge Christ's words, he immersed himself in Christ's life and actually converted into the deity. He bombed the crypt because the blasphemous forgeries had to be destroyed. When Mulder asks how his cell phone got on the dead body, Hoffman smiles. "God works in mysterious ways," he answers.

Scully stops by Mulder's apartment later that night and finds him watching Plan Nine From Outer Space for the forty-second time. Scully wonders whether true faith might be a form of insanity, and Mulder convinces her to take up Federman's invitation. The agents arrive at the Twentieth Century Fox lot in Los Angeles to see the movie's filming, and Federman introduces them to their acting counterparts - Shandling and Leoni. They watch a scene being shot in a graveyard with zombies. Back at their luxurious hotel, Scully calls Mulder from her bubble bath. Sitting in his own bubble bath, Mulder tells her that he thinks the undead really just miss the life they had when they were alive. They merely want to eat and dance and make love. Skinner clicks into Mulder's phone call to apologize for being hard on the agents. He tells him that Federman arranged for Skinner to get an associate producer credit on the movie.

Sixteen months later: The movie premiere from the beginning resumes. On screen, Shandling's Mulder professes his love for Leoni's Scully. She pulls away from his kiss and tells him she's really in love with Assistant Director Walter Skinner. The real Mulder shoots up from his theater seat, waving his arms like a referee stopping a fight. "That's it! I just can't take it anymore!" he shouts. The real Scully shushes him, but he storms out past Federman, Shandling and Leoni. Scully finds him moping on the graveyard movie set, munching popcorn out of the plastic Lazarus Bowl from the concession stand. She tells him that earlier in the evening, Cardinal O'Fallon murdered Micah Hoffman and then hanged himself. Mulder bemoans the fate of the two complex and flawed men who would now be remembered as caricatures from The Lazarus Bowl movie. He wonders how they themselves will be remembered. Scully philosophically predicts that the movie will tank at the box office, but Mulder is preoccupied with the notion that dead people will be represented through history in such an oversimplified way. Scully teases him out of his sulk, telling him that Skinner was so pleased with the movie he gave her a Bureau credit card for the night. She takes Mulder's arm and pulls him to his feet, joking that she's got a confession to make: she is in love with Associate Producer Walter Skinner. Mulder tosses the plastic Lazarus Bowl and quips, "Me too." As they walk away, a tree branch scratches against the bowl's surface like a record needle. Samba music swells, and wispy apparitions begin to dance joyfully around the graveyard set.