Mighty Mighty Missile! for the Sega Mega-CD is a license-free clone of ChuChu Rocket! that was originally released on the Sega Dreamcast. The game faithfully reproduces the presentation and gameplay of previous versions of Sonic Team, including scenes adapted from the Dreamcast and GameBoy Advance versions.

The mechanics of Mighty Mighty Missile! are largely identical to those of its parent game. Players have indirect control over the Mousers (the equivalent of ChuChu Rocket!'s ChuChus), whose trajectories must be modified through the placement of arrow tiles. The goal is to direct the Mousers past a variety of obstacles, including the Catz (KapuKapu) in their path to the missiles (rockets).
Arrows are placed using the B button and a direction on the control pad; they can be removed by pressing the B button again. When playing in Puzzle mode, the A button is used to begin the stage and also to enable fast forward playback.