When the villainous Mr. Wink and Mr. Fibb extend the adult swim time in the neighborhood pool, the Kids Next Door are sent a red alert to stop them. Numbuh 1 suggests employing the Kid-A-Pault, a Kids Next Door weapon to put an end to this tyranny...but their plan fails, leaving them to find other means of battling Mr. Wink and Mr. Fibb.
The group catches wind of some ice cream men who refuse to give ice cream to children, so they interrogate them and get the password to their ice cream factory, only to be in for a major surprise from the Delightful Children from Down the Lane, because the ice cream that they take turns into a monster that tries to eat them, but eventually gets defeated by a heater that was turned on by Numbuh 3.
The hamsters that power Sector V's weapons suddenly decide to go on vacation, leaving the Treehouse powerless! Meanwhile, the Delightful Children from Down the Lane looks for villains to attack Sector V, so they send an old lady named Gramma Stuffum, who is fixated on fattening kids, to Sector V's powerless HQ.
Numbuh 4 learns he is to be sent to a boarding school – but he is not worried, as he's always escaped from them before. However, he then learns that the school is being run by an evil kid called "Madame Margaret", a girl who is getting high-tech aid from none other than her future self. Madame Margaret's abominable plan is to create a twisted utopia where girls rule the world, using a demonic weapon called the girlifying ray that can turn anything feminine. The team does not have much chance to stop this until they receive aid from Numbuh 4's own future self. Now the team must defeat her and save the future.
The DCFDTL kidnap the team's classmate, a nerdy, spit-talking girl named Leaky-Leona and force her to lead them to the dark underbellies of the school. Alerted by Numbuh 5, the team follows them, and find themselves in an ancient school, laden with deadly booby traps. Avoiding them all, the team finds Leaky-Leona, strangely aged to an old woman, who leads them to the mythical Fountain of Youth. The KND are amazed at the prospect of remaining ten-years-old forever.
The Code Module is recovered by Sector V in time for Tommy to graduate. However, the information inside of it is used by Father to turn every single operative into an animal, leaving Tommy the last one who's not transformed into an animal since he removed his DNA from the Code Module in order to save the KND.
Numbuh 4's new pool is actually a portal to an alternate version of the KND Universe where their counterparts known as the DNK (Destructively Nefarious Kids) are evil. The kids do all the adults' job whereas the adults sit around and play video games. While swimming in the pool, Lizzie is captured by an evil opposite of herself, Eizzil Enived (Lizzie's name backwards), and Nigel follows the captor back to her home universe.
Once again, a special birthday cake is being made for the Delightful Children from Down the Lane. The KND take a trip to the Alamode where tour guide Numbuh 50 Million B.C. tells them about the 1800s KND operatives who were determined to steal the Annoyingly Cute Triplets Who Lived Upon the Hill's Birthday Cake, a delicious cake made by their mother. However, in their attempt to get the recipe, an ice cream trap was set off, freezing over 5000 KND operatives. It took 10 years to thaw them out, and all were decommissioned since they were technically too old to be KND. All were found except Numbuh 19th Century, the operative sent in to get the recipe and set off the trap, until the current KND recently discovered him. After being thawed out, he's confused by the new modern era, especially with the fact there are now girls in the KND.
Every year, the KND choose someone to be "IT" which involves a game of tag to choose the next Supreme Leader, so Numbuh 362 sets up the game after she decides to resign due to being tired of the job. However, when Numbuh 2 accidentally tags Father, he becomes Supreme Leader. Numbuh 1 and Numbuh 362 then must stop him before he wipes out the entire KND using broccoli.
In the sooper triple gihoogest Codename: Kids Next Door adventure ever, an evil more eviller than Father threatens to turn both kids and adults into tapioca-eating, hideously wrinklified Senior Citizombies. To fight this menace, the Kids Next Door are forced to recommission their greatest operative ever: Numbuh Zero! Join Numbuhs One through Five and the rest of KND Global Command as they battle alongside their bygone hero to fight for not only kids...but the world!
When a kid-friendly senator receives a funding of approximately eleventy-billion dollars, he uses it to build an army of Safety-Bots, to make the world a safe place for children. However, the robots grow more and more extreme in their actions, eventually planning to eliminate adults, and cover the Earth in bubble wrap.
Heinrich uses a ritual involving sacred golden caramels to take away the qualities the Sector V operatives value the most (Numbuh 1's leadership, Numbuh 2's intellect, Numbuh 3's giddiness, Numbuh 4's toughness, and Numbuh 5's coolness). Numbuh 5 eventually teaches Heinrich that he needs to share his candy to revert to his original form, she is then seen leaving with a young blonde girl.
The KND and the Teens are about to sign the "You don't mess with us-We don't mess with you" Kid-Teen treaty. It is going to be signed by Numbuh 8000 (KND and the Teens leader), but it turns out to be a trap for the KND, making Numbuhs 1 and 274 set out to prevent it after being falsely convicted by the KND.
Worlds collide when Billy accidentally steps into the Delightful Children's Delightfulization chamber with Grim's scythe and emerges as a hideous cross between himself, Grim, and the Delightful Children! Soon, the KND are called in to stop this Delightful Reaper's rampage across the country as it grows bigger and bigger, adding more and more children to itself to make the perfect child! With the KND leadership in a shambles, Mandy takes over the organization to fight this creature -- but may have ulterior motives in commanding her own army!
In a series of interviews with the KND after they're all grown up, the former operatives are temporarily brought out of their decommissioned haze to discuss what happened during their very last mission with Numbuh One -- the one where he disappeared and was never heard from again! It all started with a routine mission to get the Delightful Children's birthday cake, but when a mysterious boy steals it instead he makes it available to whoever wants it -- IF they can solve his 'simple' scavenger hunt first. Soon it's a mad, mad, mad, mad chase around the world as the KND, their friends, and virtually all of their enemies compete to win the yummiest cake ever while Nigel Uno is faced with the most difficult choice of his life: the KND or his friends. And the answer is out of this world.