The story of Magic Pockets follows the Bitmap Kid as he attempts to retrieve his stolen toys from various creatures. The game takes place across four worlds, each with its own unique enemies and challenges.
Gameplay involves guiding the Bitmap Kid through side-scrolling levels, using a variety of shots and abilities to defeat enemies and overcome obstacles. Charging up shots before firing can increase their damage output, while special items grant the player new skills such as bike riding, diving, and flying.