The 200th episode of South Park brought together all the characters from the previous 199 episodes, including the Prophet Muhammad, who was depicted in the "Super Best Friends" episode, wherein the major religious figures of the world comprised a Justice League knock-off. This episode was before September 11, 2001, and therefore encountered no Islamic controversy.
After the Danish cartoonist whats-his-face drew the now infamous cartoon of Muhammad as a terrorist, and the ensuing violence that followed, Comedy Central refused to show any depiction of the Prophet Muhammad. Thus, in episode 200, Muhammad was covered by a "censored" bar, hidden in a U-Haul truck, and concealed under a bear mascot costume.
Regardless of that fact, a radical fundamentalist Muslim group made thinly veiled death threats towards the creators of South Park. In the 201st episode, which was a continuation of the 200th, depictions of Muhammad were even more censored, as a joke, to the point where even the name "Muhammad" was bleeped out.
After the episode was handed off to the network for airing, however, additional bleeps were added that interfered with the satiric message of the episode, which addressed censorship and intimidation in society. Apparently, they bleeped out significant portions of one of the show's characters' final monologue (the show routinely has a "I really learned something today..." monologue at the end of each episode). This occurred without the creators' consent, and it occurred despite that monologue never mentioning Muhammad.
I and others see this as an outrageous act of cowardice on the part of Comedy Central, the network which airs South Park in the United States. Bending to fears of violent Islamic retaliation, they chose to censor the episode's message rather than celebrating the cherished ability of American artists to create and publish works that criticize society. The absurd, enraging irony in this situation is particularly acute because the events the show's creators were specifically addressing in these episodes (i.e., voluntary censorship in response to threats of violence) are precisely those events which led to these episodes' censorship.