Mario is attempting to clear the bad guys out of the "Clash Tower" after they take over in their big evil-looking blimp. He'll have to clear the place out on his own, one floor at a time.
Mario Clash is a remake of the Mario Bros. arcade game for the Virtual Boy. It features many of the same enemies as the original game, plus a few new additions like Paragoombas and Boo Buddies. Since the game attempts to show off the 3-D capabilities of the Virtual Boy, Mario is able and often required to attack enemies by tossing Koopa shells at them from opposing sides of the playing field. To make sure this is possible, there are two Koopas on screen at all times. Each stage can only be completed when Mario defeats every single enemy on screen. There is a mushroom counter on the upper-right hand corner of the playing field. It counts down once for every non-Koopa that Mario defeats. If he destroys all of them, he enters "Fever Time," where a hit from any direction with a Koopa shell will defeat any enemy and scoring is doubled.
Every few stages there is an interlude for a mini-game. Mario must collect as many coins as possible to earn extra lives.