As the mission begins he will stomp on the ground making two Item Boxes appear on each side of him and a bob-omb behind him. Wario must get to a item box before he gets to the bob-omb, or the item boxes will dissapear and he'll move elsewhere and do the same. Once you get the bob-omb he will get his bob-omb and throw it at you (although if lucky his bob-omb will hit him and count as a point), then hit him with your bob-omb and he will fly across the stage, after you've done this twice (or once if he hit himself) he will stay in the air and go to a location and drop three bob-ombs and one item box. Quickly get the item box before the bob-ombs explode, then move out of the way and he will finally fall, quickly throw the bob-omb or he will jump back up and repeat the process.
Big Bob-omb like all other bosses came from Super Mario 64 DS in the Bob-omb Battlefield level "Big Bob-omb On The Summit."