Family Guy
In the 2011 episode “Back to the Pilot,” Family Guy sends its talking baby and dog back in time, inadvertently preventing the attacks to catastrophic results and therefore boldly arguing that 9/11 and the Bush administration were Good, Actually. After going forward, they find an apocalyptic wasteland in 2016, which is accurate enough, just not for the reasons they show.
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Bones
In a very special 2012 Veterans Day episode, an unknown 9/11 victim must be identified by the scientists, which mostly serves as an excuse for overwrought speeches. In one scene, the show’s only Muslim character delivers a furious lecture to a suddenly ignorant colleague, and then everyone agrees that all work must stop until they all dramatically share where they were that day, to the victim’s complete lack of benefit.