Unlike other ports of the game, the Mega Drive version overhauls virtually all of the levels from the arcade game, while also changing graphical elements so that the game is more suited to the Mega Drive's hardware. Though the game plays almost identically (save for differing enemy placements and tweaks), it is shorter in length, and drops some audio tracks in favour of brand new ones presumably to fit the new levels. The changes are not as distinct as those found in other early arcade-to-Mega Drive conversions, namely ESWAT: City Under Siege or Shadow Dancer: The Secret of Shinobi, but they are significant enough for it to be classed as a different Alien Storm game.
Gameplay is virtually identical to the arcade version of Alien Storm. The mixture of brawler gameplay and first person sections, as well as the limited amount of weapon energy available, sets these games apart from the competition and similar inhouse games. Health restoring items are very sparse and given out randomly during first person sections.
This version also features two additional modes: The Duel, similar to the mode of the same name seen on Golden Axe, where you face off against multiple rounds of enemies in one go, and a versus mode, where two players can face off one on one. Strangely, The Duel can only be selected if there is one controller plugged in, which means it's inaccessible on emulators or official versions that are permanently set to have two controllers plugged in, such as the Steam version.
damages all enemies on screen but consumes a big amount of weapon energy. is a standard weapon attack that can be chained. It consumes a bit of weapon energy. makes the character dash. Double tapping a direction is for running. Attacking with while running or dashing consumes no weapon energy. If you keep holding the forward direction during dash attack then the character will go through the enemies, otherwise the character will stop on the first alien he/she hits. while running makes your character jump. You can do overhead attack while jumping.