Stan takes a Scientology personality quiz, and after making several allegations, the Scientologists try to convince him he is to be their new leader. Tom Cruise goes into Stan's closet and refuses to come out, and even denies the fact that he's in the closet. Meanwhile, Stan's involvement in Scientology puts a strain on his friendship with Kyle.
Stan doesn't go with the rest of his friends to play laser-tag, attempting to save up money for a new bike. He runs across some Scientologists, who encourage him to take a free personality test. Stan starts to question whether Scientology is a religion, which the auditors try to avoid. After the personality test, the auditor makes the assessment that Stan is depressed and a perfect candidate for Scientology.
At dinner, Stan asks his parents for the money for "a self-help program", telling his parents that he's been depressed and didn't know it. Randy tells him to use his bike money if he wants to join the help program.
After Stan goes through his auditing session, the shocked auditor sends the results to the home office. Due to Stan's impressive thetan levels, the president of Scientology concludes that he is the reincarnation of L. Ron Hubbard.
The president of Scientology visits Stan's home, and tells his family the news. Randy sends Stan up to his room while he talks with the Scientologists. Stan, in his room, encounters Tom Cruise who asks him what he thought of his movies. Stan's callous opinion of his acting causes Cruise to get upset and he locks himself in Stan's closet, resulting in the running joke of "Tom Cruise won't come out of the closet!"
The president of Scientology tells Stan the secrets of Scientology, the Xenu story (which is played out on the screen with the words "This is what Scientologists Actually Believe" on the bottom of the screen). The president of Scientology tells Stan that his job is to write new doctrine for the church. Stan tells him he does not know how to start, the president tells Stan that Hubbard did not know either.
As he is writing, the whole town has gotten involved in trying to get Tom Cruise out of the closet. John Travolta, another famous Scientologist, is called in but he also ends up in the closet with Cruise. During the newscast R. Kelly (singing like he does in "Trapped in the Closet") randomly sings then pulls out his gun. Nicole Kidman is brought in to try to coax him out of the closet, to no avail. R. Kelly is also called in, but also finds himself in the closet as well.
Stan presents his new doctrine to the president, telling him what is in them. When he says that Scientologists should not have to pay to be in the religion anymore, the president tells him the truth -- Scientology is a big scam.
When Stan tries to read his doctrine to the followers outside, he can't do it, and proceeds to tell everyone that it is a big scam. This makes the Scientologists angry at him, and the president tells him that he will sue Stan for saying that their religion is a scam. Stan tells the president that he stated Scientology was a big scam, but the president denies it. In the meantime, Cruise, Travolta and R. Kelly have come out of the closet, and Cruise tells Stan that he made him look stupid and threatens to sue him in England. Stan proceeds to shout after them, "Go ahead! Sue me! I dare you!"
The credits roll, with everyone named as either "John Smith" or "Jane Smith."