The Secret Files contains Jazz Jackrabbit 2 and an additional separate episode. It features nine new levels containing new textures, and enables the player to control a third character, Lori. In almost each level there are alternate routes that the player can take.

If players complete the nine levels they may try their luck in twenty other levels that were created by fans of the game, including the single-player level, "A sting in your tail!". Like the base game, this edition includes JCS, the Jazz Creation Station, where gamers have the opportunity to build their own levels.