Conspiracy Theory
Explanation
The Joke
A government aide shows the President a news report about conspiracy theorists who believe every time a plane leaves a contrail ("chemtrails") it is the government dropping chemicals. The President, rather than dismissing the theories, sees this as a golden opportunity: since conspiracy theorists already believe the government is doing these terrible things, why not actually do them? Nobody would believe the conspiracy theorists if they reported it, since they have no credibility. The President then orders a plane to drop squirrel pox on every county that did not vote for him, and when an aide objects that this is illegal, the President smugly dares her to go to the media, knowing she will sound like a conspiracy theorist herself.
The Humor
The comic inverts the usual dynamic around conspiracy theories. Normally, the humor in conspiracy theories lies in their implausibility. Here, Weinersmith flips the script: the existence of conspiracy theorists who cry wolf about government plots actually creates the perfect cover for a government that wants to commit real crimes. The absurdity escalates with the specificity of the evil plan (squirrel pox dropped on counties that did not vote for him), and the final punchline lands when the aide realizes she is trapped in the same credibility paradox that makes conspiracy theorists powerless -- even though she has witnessed actual wrongdoing, reporting it would make her sound just as crazy as the theorists.
References
The comic references the "chemtrails" conspiracy theory, which claims that the condensation trails left by aircraft are actually chemical or biological agents deliberately sprayed by the government for nefarious purposes. This has been widely debunked by atmospheric scientists.