As the smartest man in the Central Finite Curve, Rick & Morty's titular Rick Sanchez does not have much to fear. Even against advanced alien civilizations and other dimensional versions of himself, Rick always comes out on top. However, despite Rick's constant triumph, there is one animal species he fears more than anything: squirrels. It doesn't seem right that the smartest man in the universe would be afraid of acorn-gathering tree rodents, but the Rick & Morty Presents comic series shine some light on Rick's sciurophobia.
Rick's fear of squirrels is introduced in the third season's eighth episode: Morty's Mind Blowers. In this episode that serves as much like Rick and Morty's famous Interdimensional Cable, a flashback shows Rick giving Morty a device that lets him talk to animals. As Morty frolics through the neighborhood listening to animals' conversations, he happens upon squirrels discussing their dominion over the world. When they realize Morty is listening, they attack, and Morty seeks out Rick's help. He reprimands his grandson for messing with squirrels, and then it's revealed that this caused Rick and Morty to leave that reality. Rick has wiped out entire realities out of spite, yet dealing with squirrels crosses the line. Why is this?
Rick and Morty Presents: Snuffles Goes To War by Christopher Daniels, Devaun Dowdy, Leonardo Ito, and CRANK! reveals that squirrels are the secret rulers of Rick and Morty's world and have technology capable of inter-dimensional surveillance, warfare, and devastation. Seeing the planet Dogg-One and its population of dogs as a threat, the squirrels unleash mayhem resulting in a war between the two species. Not only do the squirrels have access to powerful technology, but the comic implies that squirrels being secret rulers is a universal constant.
With all this in mind, it makes sense that Rick steers clear of any drama involving the squirrels. The fact that Rick would resort to traveling to an entirely different reality rather than ending them speaks volumes to his fear. Especially since the squirrels have the technological means to go toe to toe with anything Rick could throw at them, it makes sense that he would focus his efforts elsewhere. Perhaps if Rick used the magic Hollaluog he could best them, but that goes against everything he believes in.
Rick's fear of squirrels seems like the sort of random comedic trivia Rick and Morty excels at, but the comics flesh out his phobia into something highly understandable. It's not often that Rick faces something with capabilities on par with his own, but unlike other adversaries, Rick doesn't think that he can beat the squirrels.