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The episode "Stark Raving Dad" was missing from the library of episodes that debuted on Disney's family-friendly streaming service Tuesday, according to Newsweek.
The service added over 10 million subscribers in day one alone, the company said.
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In the episode which aired in the show's third season, Jackson was the character voice of Leon Kompowsky, a patient in a psychiatric hospital who thinks he is a pop star and ends up rooming with Homer Simpson.
Showrunner Al Jean told The Daily Beast that he believed Jackson used the appearance "to groom boys."
"It looks like the episode was used by Michael Jackson for something other than what we’d intended it," Jean said in March. "It wasn’t just a comedy to him, it was something that was used as a tool.
After the HBO documentary "Leaving Neverland" aired accusations of sexual abuse against Jackson in January, the 1991 episode was removed from being aired across platforms, according to The Wall Street Journal.
In the documentary, Wade Robson and James Safechuck say Jackson sexually abused them as boys.
The show's longtime executive producer James L. Brooks told the Journal, "It feels clearly the only choice to make."
The Walt Disney Company did not immediately respond to FOX Business' request for comment.
The service has also placed disclaimers on some older films.
"This program is presented as originally created," the service warns. "It may contain outdated cultural depictions."
Some users thought the disclaimer was an admission of "racist" content, while others said it was good not to change the original content.
"Look at Disney Plus letting the people know early that their old films were racist and culturally insensitive," one Twitter user wrote.
"No need to change history and lob off like one-third of a movie, but warning people about it's a good compromise," said another.
"I think it is more productive to show how things really were instead of trying to brush it under the rug. nothing good will come from ignoring history," added another.