Even a book series with a premise as kooky as this can have upsetting moments.
- Book three: George and Harold willingly sacrifice themselves to save the world by allowing the spaceship to blow up with them inside it. They believe there's no way they'll make it out alive, and they're heartbroken over it, but accept their fates.
- Book four: Professor Poopypants descending into rage and having a mental breakdown after realising that George and Harold wrote an insulting comic about him. Cocky as he was, he just wanted to help people then, but was turned away by everyone.
- Book nine has a few:
- It's revealed that Harold's father walked out on the family when he was six, and Harold created the Captain Underpants comics as a coping mechanism. Mr. Krupp in his Captain Underpants identity is a kind of Bumbling Dad Parental Substitute for both of the boys, but particularly Harold...
- Harold getting bullied by Kipper Krupp and his goons at the gas station and the jerkass owner Billy Bill refusing to do anything to stop the bullies. Thankfully he gets his just desserts later.
- When Tippy returns back to the present in the ending of the book, he's learned that thanks to his actions Mr. Krupp never became Captain Underpants and the previous villains succeeded in their goals. Just as he's about to return to set right what went wrong, he's note crushed by a giant, zombified Harold. The final pages of the book are just shots of smoldering wreckage…and a sneak peek at the next story.
- Book ten: Tippy is basically Driven to Suicide twice, both times setting off a nuclear bomb intending to be caught in its radius. While he clearly had to go, it’s a shame how far the once well-intentioned scientist has fallen.
- Book twelve:
- After Yesterday George and Harold get brainwashed by Sir Stinks-a-Lot's Rid-O-Kid 2000, George and Harold overhear their parents noting how differently they've been acting... and they agree that they like the new George and Harold. You don't even have to be someone who is/was labeled a "troublemaker" in school to sympathize with just how awful the two feel.
- Captain Underpants lost his powers and thanks to Sir Stinks-A-Lot wiping the hypnosis from his brain, he reverted back to Mr. Krupp permanently. Even worse, Yesterday George and Yesterday Harold decide to retire the character's comics in favor of making Dog Man comics, likely ensuring that except for a few people (George, Harold, Melvin) everyone will forget him.
