Mrs. Garrison's class is interrupted by Mr. Mackey, who claims someone has defecated in a urinal in the boys' restroom. The boys find it hilarious and laugh at the euphemisms Mr. Mackey uses to explain what happened. Cartman believes the incident is related to 9/11 and forms a 9/11 conspiracy theory. But Kyle disregards this and tells him to shut up.
As the day goes on, Cartman continues to say how 9/11 was a conspiracy, comparing it to the incident with the urinal. Cartman adds that one fourth of all Americans believe 9/11 was planned, but Stan and Kyle still dismiss his claims, believing that one fourth of all Americans are retarded. Soon the police arrive to investigate the urinal case. They can't find any clues so they call the Hardly Boys, two young 'whipperschnappers' with a knack for solving mysteries, to assist them. The Hardly Boys are incompetent, and follow their erections, to find evidence.
Cartman researches 9/11 and the following day at school he shows a powerpoint presentation to the whole class supposedly proving 9/11 was a conspiracy. He frames Kyle by putting numerous false evidence, like drawing a rough picture of him floating in the sky next to the World Trade Center with a knife in his hand. Everyone believes Kyle is responsible for 9/11 and avoid him.
At South Park Elementary, a meeting is in progress, discussing that what happened on 9/11 should be gone over in the classrooms. Some staff and parents, however, believe it was a conspiracy. Soon after, the Hardly boys are brought back in, much to Mr. Mackey's chagrin.
Stan asks Kyle why the CIA are asking about him. Stan then tells Kyle he's found a website that can prove Kyle innocent of 9/11. They go to the home of the 9/11 truth webmaster, who tells them the government was responsible. The webmaster gives Kyle jars of anthrax, saying it is evidence of the conspiracy, but as soon as Kyle holds them, a SWAT team enters and takes Stan, Kyle and the webmaster away.
The three of them are taken to the White House and the webmaster is executed, and Stan and Kyle learn that 9/11 was indeed a government conspiracy to justify invading the Middle East so they could create an oil monopoly and make lots of money. George Bush tells Dick Cheney to shoot Stan and Kyle, but he misses and the duo escapes.
At South Park Elementary, Clyde admits to defecating in the urinal, but his parents tell Mr. Mackey that he had a colostomy at age five.
In Chicago outside a McDonalds, Stan and Kyle see the webmaster, alive. They chase him until he is shot once again by another man who takes both boys with him. He is later revealed to be the Hardly Boys' father. Bush and his posse appear out of the shadows and confess that they weren't responsible for 9/11. However, all conspiracy websites are revealed to be run by the government. Kyle asks why the government doesn't just tell the truth about September 11. Bush says they have but since one fourth of all Americans are retarded, they might as well let them believe the government is all powerful and would willfully commit a terrorist attack on its own country. The Hardly Boys' father questions how everyone knew they were there, and Stan puts a gun to Kyle's head. He confesses that he was the one who defecated in the urinal. The whole reason he brought Kyle along was to make him believe the incident was a conspiracy done by the government, who went along with this to make people think they are more powerful than they really are.
The episode ends with Stan being punished by Mr. Mackey, who makes him laugh uncontrollably with his euphemisms for pooping again.