This game has flavors of several different video games rolled into one. It is mostly like Xevious, being an overhead shooter against a plethora of enemies, each with a unique characteristic. Unlike Xevious, however, that only allowed you to travel in one straight path, Mega Zone periodically allows you to choose different paths. For most of the game, the player's ship flies along a river. When the river forks, the player has the option of following either fork.

The game also has elements of Scramble, in that the player fights through numerous zones in the struggle to reach the end. Where Scramble has a progress bar at the top, Mega Zone gives the player a map, and shows the player the progress along the map between lives. The main enemies of Mega Zone are giant robot eyeballs. Easily enough destroyed, they still pose a menace. Smaller eyeballs leave teardrops when destroyed, which when picked up, give bonus points and wipe out all enemies on the screen.