As a recap of the previous episode is shown, an announcement reveals that the second part won't be shown tonight, so a Terrance and Phillip will be shown in its place. At the Lazy J Ranch, Terrance and Phillip are solving a mystery with the help of their good friend Muhammad (who is censored).Having seen this, Terrance and Phillip arrive at the Canadian Broadcasting Corporation demanding the episode be re-run with Muhammad uncensored. The head of the company explains there are new rules concerning censorship. Phillip points out that Family Guy is going to show an episode with Muhammad uncensored. The head of CBC tells them that someone is probably heading to FOX Studios right now to get the episode pulled.
Cartman arrives at FOX Studios and goes up to the reception asking to speak with the FOX executives about the Family Guy episode. The receptionist tells him he has to wait. Cartman goes to the waiting area where he encounters a kid, of whom resembles Bart Simpson.
Kyle reaches a nearby diner, but everyone's heads are buried in sand. A man with a gun approaches him asking why he his head isn't buried.
Cartman tries to convince Bart to let him handle the situation alone. Bart gives in after discovering how Cartman tricked a kid into eating his parents. He talks to the executives (under the persona of a Danish boy called Danny Pocket), pretending that his father was killed after publishing a picture of Muhammad in his newspaper. He pleads for the executives to pull the episode for their own sake. They are touched and decide to get him to convince the writing staff himself.
The man with the gun gives Kyle a lift to FOX Studios (he is a Family Guy fan). Kyle asks Bart for directions, but is knocked out by the latter's skateboard after being tricked into entering a maintenance closet.
Outside FOX Studios, the President informs the press that the proposed pulling of Family Guy is forbidden and protected under the First Amendment. Naturally the media has never heard of the right to free speech and begins saying it sounds stupid.
Cartman discovers that the Family Guy writing staff are Manatees and are the only species of mammal not moved by terrorist threat. It is explained to Cartman that they have a tank full of "idea-balls". The manatees move five of them and the selected five are made into a joke. If one ball is taken out, then it makes the manatees think that they cannot use that subject. They believe in a concept that if one thing can't be used, then nothing can, so they would stop their work.
Cartman visits Bart who has Kyle trapped in a net. He explains he has an "idea-ball to steal". He sneaks in and does just this and the manatees stop working. He then goes to the FOX president saying that he shouldn't be pushed around by manatees. He decides that he should pull the episode (however he finds this difficult).
Kyle has had a talk with Bart and has managed to break free after telling him he is on a slippery slope which will make him as horrible as Cartman. Cartman and Kyle then have a fight (which involves them slapping each other). They fight all the way across the studio (including smashing through the King of the Hill studios. Then Cartman says he gives up, but he kicks Kyle in the balls, knocking him down. However Bart shows up to help Kyle, and knocks Cartman out with his skateboard.
Kyle reaches the FOX president's office, telling him he shouldn't pull the episode. Cartman arrives with a gun, but after giving a small speech about not giving into terrorism, Kyle wins to Cartman's anger. Cartman then attempts to shoot the president and Kyle but the gun has no bullets.
The episode airs and all it features is Muhammad giving Peter Griffin a "salmon-football helmet".
Despite the scene not having been much, the terrorists retaliate with a short cartoon showing American people (such as the President and Tom Cruise) defecating on each other, as well as Jesus defecating on all of them and the American flag. The terrorist comments that it was way funnier than Family Guy. In turn, it raises the question, "why is THAT okay to show, while an image of Muhammad, just standing there, looking normal, is not?"
On April 13, 2006, Comedy Central issued a statement confirming that the network prohibited the show's creators from airing an image of Muhammad, saying, "In light of recent world events, we feel we made the right decision." Kyle's impassioned plea to the President of Fox was directly taken from the creators' own arguments against the censorship of Muhammad. Kyle even calls the president 'Doug', a reference to Doug Herzog, a Comedy Central executive.
Muhammad had previously appeared in the episode "Super Best Friends" and has appeared briefly in the opening sequence since that episode, including in both episodes of "Cartoon Wars", despite the controversy surrounding the two-parter.
Trey Parker and Matt Stone have clarified their opinions on Family Guy on the DVD audio commentary, Parker stated "we totally understand that people love it, that's why we put it in the show, we understand that it speaks to some people and it can just be a simple laugh and that's great and we certainly don't think it should be taken off the air or anything like that, we just don't respect it in terms of writing", later referring to the writers behind the show as "smart" but emphatically criticizing their overuse of "gag-humor".