Mr. Mackey is determined to find out who took a crap in the urinal, while Cartman manages to link it to 9/11, causing Stan and Kyle to find the truth behind this terrible event in history.
Ms. Garrison's class is interrupted by Mr. Mackey, who explains someone has defecated in the boys' urinal. The boys find it hilarious and laugh at the words Mr. Mackey uses to explain what has happened. Cartman believes it to be a conspiracy, like 9/11 was in his belief, but Kyle tells him to shut up.
As the day goes on, Cartman continues to say how 9/11 was a conspiracy, like the problem with the urinal. He says one fourth of Americans believe it to have been a conspiracy, but Stan and Kyle believe that one fourth of Americans are retarded. The police soon show up, but they cannot explain what has happened and call on the Hardly Boys to assist (two young whipperschnappers with a knack for solving mysteries). They merely follow their erections however which they call 'clues'.
Cartman decides to research 9/11 himself, and in show and tell next day he shows a powerpoint presentation on how 9/11 was a conspiracy, and frames Kyle by drawing a rough picture of him floating in the sky next to the World Trade Center with a knife in his hand. Everyone then believes Kyle to be responsible for the situation and try to avoid him.
At his home, Sheila is shocked to hear about what has happened to Kyle and decides to go to the school.
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 to be a conspiracy as well. Soon after, the Hardly boys are brought back in to Mr. Mackey's annoyance.
Stan asks Kyle why the CIA are asking him about Kyle. Stan then tells Kyle he's found a website that can prove Kyle innocent of 9/11. They then go to the house of the website's 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. George Bush then tells Dick Cheney to shoot Stan and Kyle, but misses. The duo escape and run away.
At South Park Elementary, Clyde admits to having defecated in the urinal, but his parents tell Mr. Mackey that he had a colostomy at age five.
Now in Chicago outside a McDonalds, Stan and Kyle see the webmaster, who they chase. He is shot by another man who tells the boys to go with him. He turns out to be the Hardly Boys' father. Bush and his group turn up and reveal it wasn't them who did 9/11, and it was Muslims. All conspiracy websites are revealed to be run by the government. Kyle asks why they don't just tell the truth, Bush says they do but since one fourth of Americans are retarded they might as well let them believe the government is all powerful and can commit a terrorist attack. The Hardly Boys' father questions how everyone knew they were there, and Stan puts a gun to Kyle's head and reveals he defecated in the urinal. The whole reason he took Kyle on the adventure was to make him think it was a conspiracy done by the government (who went along with this to make people think they were all powerful).
Stan is then punished by Mr. Mackey, who makes Stan laugh from his choice of words again.