In Operation: M.U.N.C.H.I.E.S., Sector V went to great lengths to acquire this cereal when they run out during breakfast. They initiated battle with other adult villains in the Supervillains Supermarket & Deli in the hopes of retrieving the last box that was currently in stock. When Knightbrace hailed as the victor in buying the box via check-out, it was revealed that he despised the cereal due to its sugary contents being detrimental to dental health, and bought it in order to destroy it. This prompted both Sector V and the villains to propose a temporary truce in order to take down Knightbrace and in the end, ultimately shared the cereal amongst themselves.
The cereal also made an appearance in Operation: C.A.N.Y.O.N., when Numbuh 4 visited the previous supermarket to order truckloads of them to fill the Grand Canyon up in celebration for the Global KND Anniversary.
Over the course of the series, Rainbow Munchies would be shown periodically eaten by KND operatives from time to time, though it had another prominent appearance in Operation: H.O.M.E., where it was discovered that the sugary contents are made from shredded Rainbow Monkey dolls that were left behind by children due to their old age. This plot was being masterminded by Nurse Claiborne herself. This haunting revelation was soon rectified due to Numbuh 3 and Numbuh 5's involvement and after an ensuing battle, punished the defeated Nurse Claiborne by forcing her to repair every single Rainbow Monkey she mangled. It is unknown if rainbow monkeys was always one of the ingredients for the cereal.