Mega Missile is a color based tile shooter. Tap the screen near the four launchers at the bottom of the screen to shoot missiles. Shoot tiles of matching colors to get points. If the missile and the tile do not match in color you will lose a heart. Destroy the tiles before they reach the bottom of the screen.

Some tiles will contain the following bonus items that are triggered or earned when the tile is destroyed:

- Bomb -> This bonus will destroy all nearby tiles.

- Reverse -> This bonus will push all tiles back towards the top of the screen to buy you some time.

- Double -> This bonus will double all new points earned. This bonus will stay active until you lose a heart.

- Heart -> This bonus will replenish one heart.

Occasional you will also notice a "Mega" Missile. When launched this missile will pass through multiple tiles without being destroyed. If you destroy multiple tiles of the same color you will gain extra points.

The settings menu includes the following:
- Two difficulty settings
- Sound effects mute button
- Music mute button