The Candy Conspiracy is one of a series of four Spy Kids Learning Adventures. In this episode, the Spy Kids, Carmen and Juni, are assigned to investigate why it is that kids in North America have suddenly stopped caring about playing and all seem to be eerily focused on chores and schoolwork. The Spy Kids perform an epidemiological study of incident reports and find that the Sueno Dulces Candy Company must be behind the behavior somehow. So the underage agents mount an invasion of the factory.

The game unfolds in an animated comic book manner. In order to accomplish the mission, the player guides the Spy Kids through 2 types of challenges. In the first, the game comes with a separate puzzle book (either printed or in PDF format) which can also be downloaded from the publisher's website. The book contains math and logic puzzles. The player will be prompted at various junctures for the answers to certain puzzles in order to advance the storyline.

The game also contains 8 minigames tied to the story: Incident Reports (a sort of epidemiological study and block game), Clue Wrappers (a pair-matching game), Taffy Canons (a Simon-style memorization exercise), Jaw Boulders, Word Steamer, Complete The Code Pattern, Encryption Engine, and Robot Rundown.