Kenny and his pet chimpanzee are asked by a mad scientist to watch over his collection of samples of deadly diseases.

When the villainous Mr. Wink and Mr. Fibb extend the adult swimtime in the neighbourhood pool the Kids Next Door are sent a red alert to stop them. Numbuh One suggests employing the Kid-A-Pault, a Kid's 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 enemies of the Kids Next Door, led by Father, join forces to resurrect the Ultimate Evil, Grandfather, a tyrant who once ruled the world many years ago when most of the villains were themselves kids. When Grandfather uses his reality-warping powers to reconquer the world and transform every human on the planet into his obedient "Senior Citi-Zombies" slaves who are forced to make Tapioca to refuel Grandfather so he can find and destroy the Book of K.N.D. The Kids Next Door are quickly overrun and transformed. It falls upon Numbuh 1 to locate the KND's only hope for salvation, the legendary hero Numbuh 0. In the process, Numbuh 1 learns some startling revelations about the origins of the KND, his arch-enemies Father and the Delightful Children From Down The Lane, and even his own family history.

The show starts off with a live-action interview of Abigail Lincoln (now Abigail Gilligan) (Numbuh 5) and the rest of Sector V. Even though they are now adults, they are told by an unnamed, unseen interviewer that the effects of decommissioning have been temporarily reversed so they could be interviewed on their final mission.