Muhammad In South Park

In Islam, it is blasphemouse to depict Muhammad. It it also blasphemous to depeict other religious figures (which explains why Islmaic extremists and radicals also destroy Buddhist and Christian statues). It is related to the commandment against idolatry in the Ten Commandments.
In the West, we tend to ridicule idolatry without destroying the statues. Since we value our freedom of religous speech, we feel it is within our rights to express that speech by depicting religious figures and allowing them to be worshiped, while also making fun of the people who worship them. To be told that we can't depict religious figures or to let them be destroyed is to let our freedom of religous speech be attacked, and we just can't have that.
This is the fundamental struggle between the West and Islam, the backdrop on which Muhammad's role in South Park has evolved. Here are the five episodes in which Muhammad has appeared, how Comedy Contral has responded to that, and how world events have changed how Muhammad is depicted on the show.

Episode

Matt and Trey's Actions

Comedy Central's Reaction

Matt and Trey's Response

The Super Best Friends Muhammad was depicted like any other character was. Being a Super Best Friend, he was given the superpower of fire in his hands. Comedy Central had no issue with this, so Muhammad wasn't censored in any way. Matt and Trey were pleased.
The events of 9/11/2001 changed the world in such a way that senstized us to the Muslim faith, but that didn't affect reruns of "The Super Best Friends." Muhammad continued to appear in the opening credits as well. In the winter of 2006, riots broke out around the world after Muslims learend of depictions of Muhammad posted in the Danish newspaper Jyllands-Posten on September 30, 2005. This hit home when Isaac Hayes asked to be released from the show after "Traaped In The Closet" aired the previous fall. He was disappointed with what he perceived as a growing insensitivity towards personal spiritual beliefs, not only with "South Park" episodes but also the Danish cartoon controversy. After Matt and Trey dealt with Hayes in "The Return of Chef," they dealt with the cartoon controversy in the following episodes.
Cartoon Wars, Part I
Cartoon Wars, Part II
In Part I they showed the townsfolk burying their heads in sand so as not to have anything to do with Muhammad being depicted in Family Guy. In Part II they put censor bars on Muhammad until it was time to depict him. When the Family Guy clip started, Trey had Muhammad appear at Peter Griffin's door to give him a football helmet with a salmon on it. Since that was the end of the episode, Muhammad, with or without the censor bar, didn't reappear. Comedy Central let the clip play, but completely blacked out that scene. Trey added some text on the black screen explaining what was supposed to be happening, and why it wasn't showing up.
"The Super Best Friends" continued to be rerun without incident. Muhammad continued to appear in the opening credits for the next two years. When Season 12 began, the show got a new opening sequence, and Muhammad was no longer part of it. Matt and Trey waited two more years to return to Muhammad in an episode or two - hopefully it would be okay to depict Muhammad again.
200
201
They put censor bars on Muhammad until it was time to depict him. This time, Muhammad was supposed to be in a bear suit, but Santa popped out of it instead when the time came. Muhammaad was back behind the censor bar for the rest of "201," and even Tom Cruise got a censor bar so he wouldn't be mocked either. That was temporary, as it disappeared after Stan said "Tom Cruise has Seaman on his back." Since Muhammad did not appear, there was no blacked-out scene as there was in "Cartoon Wars, Part II." Instead, Comedy Central bleeped out the speeches made by Kyle, Jesus, and Santa at the end of the episode. Trey was pissed off that Comedy Central would bleep out the speeches the way it did, since none of them mentioned Muhammad.
"The Super Best Friends," "200," and "201" were pulled from the South Park Studios streams and from Comedy Central reruns. This was the result of warnings from Revolution Muslim about the fates that awaited Matt and Trey if they went ahead and depicted Muhammad in "201." Revolution Muslim also published details about a home Matt and Trey co-owned in Colorado, and listed the addresses of their production office in California and Comedy Central's New York office. Security around the New York office was beefed up for quite a while after "201" aired. When Hulu took over the streams, it didn't get permission to stream these epsiodes. "The Super Best Friends" continues to be available on the Season 5 DVD sets. "200" and "201" continue to be available on the Season 14 DVD sets in the United States and nowhere else. Matt and Trey have not mentioned Muhammad since season 14, and will end the show without mentioning him again.

The bleeped speeches? The unbleeped versions appeared on January 31, 2014, after a 4chan user realized that the uncensored episode existed on the official website's web server and could be downloaded using rtmpdump (This has likely changed now that Hulu is powering the streams). That user downloaded the file and leaked it.