First of all, background info:


"Some years ago", a prominent warrior named Max lived on Phantarion. He fought against the Fiendish Bombers, who attacked the planet with a similar scheme to what they used in Bomberman Tournament. Max fought them off, but was badly damaged when he battled Brain Bomber ("Maybe he was killed
in an explosion." "[Brain Bomber] and Max stabbed each other before, but the forces of evil won!"). Somehow or another, he was rebuilt into MAX, the Bomber-cyborg we all know.

Now, in the present. A year ago, the Fiendish Bombers return, with the same exact scheme that they used the last time. However, now they have preparations with which to counter the forces of Phantarion - namely, they freeze Fairy Palace and steal the four Medals before the people can react, giving the Fiendish Bombers the upper hand. Max is sent there, but Plasma Bomber turns into Plasma Roc (it's not "Rock", it's "Roc", like the bird) and beats him down. Then Bomberman comes into play and so on and so forth.

So in the ending sequence, Brain Bomber is beaten, the Ultimate Weapon is destroyed, and Fantasy is restored to its original form (it had been corrupted by Brain Bomber). Queen Emeralda thanks Bomberman and Max for saving their planet. For a moment, she thinks she recognizes Max (our Max) as being the warrior Max who was "lost" so long ago, seeing his eyes through the visor of his helmet. Then she returns to Fantasy to rule the planet (as holo-Max said once in the game, she used to "rule this place" from Fantasy; Fairy Palace was sort of a hideaway place for the royalty to move to when under attack. It worked last time, but this time the Fiendish Bombers were prepared and sealed them within the palace).