Deputy Dangerous and Danger Dog plan to gain super powers by draining them out of Captain Underpants, using the Deputy's "Super Power Taker-Awayer Ray 2000". They are successful and the powers are turned into juice. When Dangerous is about to drink the juice, the police arrive. However, Danger Dog had already drank some of the juice at this point and the two villains escape (Captain Underpants remains at the Laundromat due to the cops being more focused on Deputy Dangerous and Danger Dog).
Meanwhile, Mary Hoskins gives birth to a boy and the doctor has to give him the spank of life (as it is a tradition according to the doctor). The spanking accidentally shoots the baby out of the window, and the baby lands in the bucket of super power juice that Deputy Dangerous was stealing. The baby drinks the juice, causing him to gain super powers. Dangerous tells the baby to "give him the juice back", but the baby doesn't respond, instead beating Dangerous up. A nurse appears and gives the baby a diaper. The baby then flies up to the ward where he was born. The doctor tries to apologize for the accident he caused, but Billy then goes and spanks him a lot to make the accident forgiven. After seeing this, Bill Hoskins, decides to name their son Billy due to him being tough like him. The family returns home, but Deputy Dangerous and Danger Dog are arrested.
Due to Danger Dog's super powers, the duo escape from the jail they were placed in and head to a secret lab. Deputy Dangerous then invents the "Danger Crib 2000", a crib that can zap super powers from babies and transport them to the user via satellite. They send it to the Hoskins family under the pseudonyms "Deputy Un-Dangerous" and "Safety Dog". That night, Deputy Dangerous gets ready to gain the super powers. But then, Billy unknowingly poops in his diaper one minute before the transmitting time (Midnight). Mary appears and takes Billy out of the crib just in time, so she could bathe him, which causes the poop to be transported over to Deputy Dangerous, turning him into a piece of poop.
Deputy Dangerous is shocked by this and goes down to the city for some thinking. After a while he gets an idea, but gets squished by a passing man. He then scrapes Dangerous off with a stick and throws it into the trash. Dangerous survives and vows to get revenge. On the way back to the lab, Danger Dog says some poop jokes that angrily provoke Dangerous so much that he soon yells out angrily and comically "I'll kill You!" at Danger.
The next morning, Deputy Dangerous invents the "Robo-Ant 2000" so he can take over the world. He then asks Danger Dog's opinion about his new robot, but Danger Dog only asks if he can Dangerous "Deputy Doo Doo" from now on. He gets angry at this and tells he won't think it is so funny after he destroys the world. He then unleashes his robot on the town to cause havoc around the city. However, Danger Dog instead goofs off by switching signs around and taking out parts of it. Billy hears about the robot from his parents, and decides to stop it (since he thought it was an actual bug). Despite his best efforts, Billy is defeated by Dangerous and he takes Billy to a Nuclear Power Plant to kill him with the radiation. Danger Dog saves Billy, while the Ant loses balance and falls into the power plant instead.
Danger Dog then takes Billy home. Bill and Mary consider keeping Safety Dog as a pet, but the Landlord disagrees, saying that Danger Dog might pee on the carpet. Bill and Mary then ask the Landlord that Danger Dog might wear a diaper, and this causes the Landlord to change his mind. Danger Dog changes his name to Diaper Dog, and becomes part of the family.
Meanwhile, back at the power plant, radioactivity from the reactor causes Deputy Doo-Doo to grow into a giant, causing him to break out of the reactor and resume his rampage 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 as they could get mutated from the radiation. Instead, they trick him to attack himself, and they eventually wrap him up using a giant toilet paper roll (taken from the top of a building. They also had to apologize to the owner of the store for it.), and dispose him onto the planet Uranus.
On the way back to Earth, they stop by at a Starbutts on Mars, where they discover that the store offers super power juice. They decide to take some back to Earth, and they go to the Laundromat where Captain Underpants is still held captive. They restore his powers, and all is right with the world. Billy and Diaper Dog return home to their parents where they all share a group hug.
- Billy was originally going to be named Spanky, due to him spanking his doctor (this is referenced in the doctor's quote "You should have named him 'Spanky'"). However, Dav Pilkey decided to rename him Billy so that he can have his parents say the lyrics to "Billy, Don't Be a Hero" by Bo Donaldson and the Heywoods.
- Billy and Diaper Dog are seen in Captain Underpants and the Big Bad Battle of the Bionic Booger Boy Part 1: The Night of the Nasty Nostril Nuggets. When Melvin is reading the comic about himself, they are both seen entering and leaving jail.
- In the "Flip-O-Rama" sections, every few pages contain an instructional paragraph about which pages to flip. The first few Flip-O-Ramas say the same thing, but eventually the paragraphs contain other information, such as silly jokes and hidden messages from Dav Pilkey.
- Starbutts would be a parody of Starbucks.
- When Deputy Doo Doo looks in the mirror he says, "What the...I'm a piece of poo!" But the reflection says: "What the...he's a piece of poo!"
- This book contains a few pop culture references, like when Diaper Dog says, "When we get home, will you read me Winnie the Pooh?" and Dial 'R' for Revenge is a parody of Dial 'M' for Murder.
- A running gag in this book is the Deputy Dangerous is called Deputy Doo-Doo from chapter 3 onward and he gets annoyed by this which often follows up with him telling characters including the narrators to not call him that.
- In the sequel to this book, after George and Harold show this book to Mr. Krupp as their 100 page essay, he is shown ripping this book up after he read the book and found out what it was about. This does not explain how the book is completely intact with no rips shown since after the backstory is explained, the book is shown undamaged, though it is possible that George and Harold created another copy of the book to show to the public. Also George and Harold are showning reading Mr. Krupp's version of How the Grinch stole Christmas shortly after Mr. Krupp tells them they should make a story based on something else that isn't offensive to him after ripping this book up, but the prologue of this book shows them writing sentences in the detention room for creating an offensive comic book after showing this book to him. It is possible they read the book after doing their time in detention since the comics that explain backstories skip a few events and details that are not relevant to the subject at hand.
- In this book the toilet paper company owner Bob is African American, but in the sequel to this book, he is shown as a Caucasian.
- Deputy Dangerous at one point states "I'm going to get you Super Diaper Baby! And your little dog too!". This is a reference to the Wicked Witch of the West's famous phrase in The Wizard of Oz.