The comic's name is a pun on the German tale "The Pied Piper of Hamelin."
The comic in the book starts with an introduction of Professor Poopypants. By getting laughed at by the children, he is infuriated and decides to get revenge on them for that. Poopypants builds an army of Gerbil-Jogger 2000s and puts a gerbil in each one. However he can't make them do any evil stuff, so he puts some headphones on the gerbils and played Cher on the headphones which made the gerbils obey his commands. They all head for the school and attack everyone in it (Including the gym teacher. They also knocked down some cupcakes during their rampage). Professor Poopypants then rounds up the kids and uses the children as slaves, but Captain Underpants appears and, along with the children (and even the gerbils), he laughs at Professor Poopypants's name after he says what it is. Professor Poopypants then presses a button on his bowtie, which transforms him into a giant cyborg. Captain Underpants then fights him for a bit before Robo-Pippy follows him to a junkyard. There, he catches ahold of our hero before proceeding to use a device (Known as the Big Crusher Thingy 2000) to crush Captain Underpants. Captain Underpants, however, uses a rather small toilet (Known as the Tiny Toilet of Truth) to rust Robo-Pippy. Captain Underpants also squashes a radio reading Cher's Greatest Hits, which was controlling the gerbils (as they were wearing headphones). Captain Underpants takes Professor Poopypants to jail as the comic ends.
At the end of the comic, there is a notice reading "All animal cruelty was simulated. No actual gerbils were forced to listen to Cher".
- The part where Professor Poopypants' bowtie transforms may be a parody of Transformers.