The story begins when a girl named Leona is using the bathroom at school. She's about to use the sink until a minion of the Delightful Children from Down the Lane grabs her. The DCFDTL demand to know where it is (obviously, we don't know what it is, yet!), but Leona tells them she doesn't know what they're talking about, until the minion, whose name is Lunk (not to be confused with the Six-Gum Gang member Lunk), gives Leona a swirly. Leona tells them it's in the sink. The DCFDTL pull the faucet and a passage opens and they take Leona with them. The Delightfuls order Lunk to make sure uninvited guests do not interfere with their plans.
Lunk looks at one of Leona's bracelets (which was dropped after the DCFDTL dragged Leona with them), and then, Numbuh Five hits him with a stall door and summons 4 more uninvited guests-- her teammates: Numbuhs 1, 2, 3 and 4. Numbuhs 1, 2 and 3 are busy with their schoolwork, but upon realizing they're being called on a mission, they leave out dummies of themselves (Numbuh 3 just leaves a balloon that says "me" on it). Numbuh 4 is busting out of school, but is called on the mission. Numbuh 5 tells her friends what happened. Numbuh 4 wonders what the DCFDTL want with Leona, and that he thought they were called for something important. Numbuh 5 tells them that operatives of the KND were supposed to save kids. The kids head down the stairs through the secret passage.
The KND end up in a really old school buried beneath theirs. Knowing they can't talk really loud, they learn they're in an old library. Numbuh 2 and Numbuh 3 find one of Leona's bracelets on the ground. Numbuh 3 begins to blab about the uses for the bracelet (not to mention, talking really loud!), then Numbuh 1 grabs it, and accidentally tosses it at a bookshelf, destroying it, causing the room to shake and the exit starting to seal. The KND make their way to the exit and manage to escape the old library. The KND find another one of Leona's bracelets and continue the trek.
They visit the cafeteria. Numbuh 5 tells them not to touch a thing there. Numbuh 1 tells Numbuh 4 "Numbuh 5 says 'Don't Touch Anything'!", Numbuh 4 tells Numbuh 3 "Numbuh 1 says 'Don't Punch a Thing'.", and Numbuh 3 tells Numbuh 2 "Numbuh 4 says 'Try the Onion Rings.'". Numbuh 2 begins to grab the food, and sets off a trap. Milk starts to flood the cafeteria, until it makes a tidal wave. The KND manage to escape the deathtrap, and Numbuh 4 demands to know why they must rescue Leona. Numbuh 5 tells him the last time the KND failed to rescue a child kidnapped by the DCFDTL, they did something the KND will never forgive. Numbuh 4 asks them what the DCFDTL did. Numbuh 1 tells him the DCFDTL made him bald!
After the cafeteria mishap, the KND wind up in the gymnasium. Numbuh 2 accidentally activates a booby trap and statues block the exit. Numbuh 4 says that gym is the one thing he can handle. He throws a ball at the statues, and the statues do the same. The KND are about to escape, but a wall of fire blocks the way. Numbuh 4 eventually wins the Dodgeball game and continue on.
The kids find Leona, to find that she's starting to age. Leona tells them to get her to the fountain of youth.
After finding Leona, they learn that they must get her to the Fountain of Youth. The Sector V Team realizes if they visit the Fountain of Youth, they could be 10 years old forever. They get Leona untied and are about to get her to the fountain until the Delightfuls appear and tell the KND that every kid's goal in life is to grow up, and that the Delightfuls are intent on destroying the Fountain of Youth. The Deligthfuls bring out their Really Really Incredibly Destructive Machine, and then a battle begins. Numbuh 5 distracts them and pillars start to fall on the Really Really Incredibly Destructive Machine. Though it survives, it short-circuits and the DCFDTL turn to babies.
After that, they get Leona to the fountain and Leona turns into a kid. Leona tells the KND she found the fountain 300 years ago. The effects of the fountain are temporary and Leona couldn't go all the way through school, so she repeated the fourth grade over and over again. Leona thanks the KND for rescuing her, but now, she has to destroy them. She starts squirting the KND with the fountain water, turning them into babies. The DCFDTL (still babies) reemerge in their Really Really Incredibly Destructive Machine and cause the bridge to the fountain to be destroyed. The KND are on the other side, and Leona's about to fall from the bridge. Numbuh 5 says the mission is over, and that they should leave. Leona wants them to help her, because she should've trusted the KND, but Numbuh 5 refuses, until Numbuh 4 convinces her to save Leona. The KND save Leona, and the fountain is destroyed.
Returning to the Girl's Bathroom, Leona thanks the KND for saving her. The KND ask Leona what she'll do without the fountain as they resume their normal ages. Leona says it's okay, because she's been a kid longer than most people have been alive. The KND leave and Numbuh 5 gives Leona her bracelets back. Leona turns back into her adult self and they leave the bathroom. The DCFDTL exit the Fountain of Youth, too.
While walking in a hallway, Leona looks at a really old drinking fountain with green water coming out. She uses it, and then, leaves the school a kid again.