Stan is saving his money for a new bike and as a result he doesn't join Kyle, Cartman and Kenny when they go off to play Laser Tag. Opting for something that is fun and free, Stan takes a personality test that is being offered by the Scientologists. After answering a lot of questions the results of Stan's test show that he is one messed up kid who is "completely miserable and totally depressed." Something that Stan wasn't aware of. Fortunately it makes him a perfect candidate for scientology and for only $240 they will help him out. Back at home, Stan asks his parents for the money to help him with his total depression. His father suggests that he use the money for his bike money, it's his choice, does he want the bike or does he not want to be depressed. Stan takes the plunge and spends his money on Scientology. Stan gets a brief history of Scientology before he goes into auditing room where his "Thetan Levels" are read. Stan grabs hold of the device and his levels are off the chart. After trying four different E-Meters, the results are the same. His results are faxed to the headquarters in Los Angeles, where Scientology's president reviews the results. Stan has registered an OT9, the only other person to score that high was L. Ron Hubbard, Scientology's founder and prophet. Back in South Park Stan is taking out the garbage when he sees that a large group of people have gathered outside. The Scientologists have gathered there to celebrate Stan as the reincarnation of L. Ron Hubbard. The president of the group arrives and goes inside to talk with Stan's parents. His parents are against him joining the group, but the president tells them that they are looking for Stan to lead their group. John Travolta has arrived on the scene. Randy sends his son to his room. In his room Stan finds that Tom Cruise is there waiting for him. When Stan tells him what he thinks of his acting, Tom goes into the closet, believing he has failed in the eyes of the prophet. Stan calls for his father's help and Randy tries to get Tom Cruise to "come out of the closet."
Four hours later Tom is still in the closet. Everyone wants him to "come out of the closet." R. Kelly is on the scene and sings about Tom Cruise being in the closet. The scientology president tries to convince Stan's parents to let them have their son. They want to reveal the great secret of life behind their church to Stan. Randy asks his son if he would like to know this information and Stan responds with a "sure." Usually it takes several years before a member can hear this information, but Stan is on the fast track. The president tells him what the Scientologists actually believe, involving aliens from about 75 millions years ago coming to Earth. Now what the scientologists want Stan to do is pick up the story where L. Ron left off. Meanwhile, upstairs Nicole Kidman is trying to get Tom to "come out of the closet." Tom continues to deny that he is in the closet. Stan begins writing and when Kyle, Cartman and Kenny come over to invite him to the movies he doesn't have time for them. Kyle is concerned about the cult that Stan has joined, but Stan assures him that Scientology is based on fact. If they can't accept that he has found meaning (instead of the depression he didn't know he had) then they are no longer friends.
John Travolta also tries to get Tom to "come out of the closet," but instead he finds himself joining him. Out on the street R. Kelly sings about this latest development. The Scientologist president is reading Stan's new work and when Stan tells him that he thinks that that church should no longer have to pay money to belong to the church; then the president tells him what the real deal is. There is a lot of money to be made from their followers. R. Kelly goes upstairs to try to get Tom and John to "come out of the closet." R. Kelly gets angry, pulls out his gun, and when the closet door opens, he finds himself going inside. Outside, the president introduces Stan, who is going to read to them from his new doctrine. Stan goes over some of the highlights, but decides that he has to come clean with his followers. For his efforts, all his followers plan on suing him. Even Tom, John and R. Kelly have all "come out of the closet," with plans on suing Stan. Stan tells them "I'm not scared. Sue me!"