The actual game-play itself is somewhat different from its predecessor, Bomberman Generation. Instead of playing as just Bomberman, players can switch between him and his partner Max, whose addition to the gameplay is the use of the Hyper Plasma Bomb to destroy certain walls and destroy all on screen enemies, which is also useful for some bosses. He cannot use Charaboms, as Bomberman can. You cannot pick a world to start from as in Generation, they must be played in order.
The Charabom usage is different from that in Generation. Instead of Pokémon-style battles to acquire them, they are either hidden in certain levels or held hostage by the Hige Hige Bandits or other enemies. Some have different effects than in the first game, and those effects are increased the stronger the Charabom becomes. Some charaboms are required to progress through a stage or collect hidden items. There are also about 16, versus the 18 seen in Generation (including hybrid Charaboms). However, unlike Generation, Charaboms can evolve, much like a Pokémon does. When a Charabom evolves, its appearance changes, sometimes drastically, and its ability may become stronger.
Attribute Bombs are again in use, though they have much different effects and can only be put down one at a time.
Mujoe and The Hige Hige Bandits, sick and tired of Bomberman repeatedly stopping their plans at galactic conquest, enact a plan to do away with him and his kind forever; Dark Star, Mujoe's artificial comet, would be used and hurled straight into Bomberman's home world, Planet Bomber. The resulting collision would completely obliterate the planet and all who were still on it. Dark Star will hit the planet in under 24 hours, so Bomberman and Max are sent out to deactivate the huge engines propelling the comet through space, thereby disabling its flight-plan and again thwarting the Hige Hige Bandits.