After Mr. Krupp bans Captain Underpants comics, George Beard and Harold Hutchins decide to create a new comic book called "Super Diaper Baby." After seeing the comic, Mr. Krupp is shocked and sends them both into detention. In the sequel introduction it shows what happened after Mr Krupp reads the first book (as well as giving us a quick reminder or glimpse of what happened in the first book like in all the Captain Underpants books except the first) it turns out he rips it up and throws it away and shouts at George and Harold at to why can't they write about something besides poop, but they can't think of anything so to help Mr. Krupp gives them the book: . It had the final seven pages ripped out and Mr. Krupp said it is because it is more realistic like that. After reading it George and Harold are inspired by the book and enjoy it. They then decide it was the right thing to write about other things than poop. After a while they decide to make a sequel to the previous book which was about poop and make this one about pee and when they give it to Mr. Krupp he sent them into detention again and he make them do busy work.
Mr. and Mrs. Hoskins, Billy and Diaper Dog go to the park to set up a picnic, Mr. Hoskins plays "airplane" with Billy, but Billy gets carried away and attempts to play the same game, tossing his dad into a tree thanks to his super powers. Mr. Hoskins tells his son everything is okay, puts an ice pack on his head, and starts eating with the rest of the family. Then, a girl appears and asks Mr. Hoskins to help her get her doll back because a bully stole it and was about to smash it with a rock. Before Mr. Hoskins can reply, Diaper Dog grabs the bully and forces him to apologize and return the doll to the little girl. Then, a boy and a girl ask for help getting their ball, which is stuck on top of a . Before he could help, Billy cuts in and becomes Super Diaper Baby to push the portable toilet down so they could have their ball. Unfortunately, the toilet was occupied, and an innocent bystander was exposed. Last, a mother of a child asks Mr. Hoskins if they can drive them to the hospital because her son had a broken toe due to playing kickball. Before he could help again, Super Diaper Baby and Diaper Dog cut in and take the two to the hospital in less than 5 seconds. That night, Mr. Hoskins feels depressed, saying he doesn't seem "important" for what he does because he doesn't have super powers. Mrs. Hoskins tries to cheer up her husband by telling him he's still good at reading bed time stories, so Mr. Hoskins decides to read a book called "Mechafrog and Robotoad are Enemies" to Billy. But Diaper Dog explains that the super powers he has gave Billy the ability to read. And Billy reads the book to his sad father.
Meanwhile, back at the power plant, causes Deputy Doo-Doo to grow into a giant, and he resumes rampaging through the city. Super Diaper Baby and Diaper Dog fly out to stop him, but Diaper Dog notes that they shouldn't touch the now-radioactive Deputy Doo-Doo. Instead, they trick him into attacking himself, and they wrap him up using a giant toilet paper roll (taken from the top of a building called "Bob's Toilet Paper Co."), and remove him to the planet .
At the city, Super Diaper Baby and Diaper Dog discuss Mr. Hoskins' blues. They also take down a purse snatcher, a carjacker, and a swindler while they talk. Diaper Dog finally announces they will try a find a way to cheer him up.