The Bomberman universe was created by the Angel of Light and Shadow, who was somehow split into two halves: A goddess named Mihaele, and a demon called Sthertoth. Sthertoth brought darkness to the universe, but Mihaele gathered warriors to fight the darkness and seal Sthertoth away in the Celestial Stone. She then hid the stone on Planet Kaos to prevent anyone from finding it.
Unfortunately, two space pirates named Lilith and Rukifellth arrived and found the stone. When Rukifellth touched it, his body was taken over by Sthertoth. He brainwashed the seven Elemental Knights, Baelfael, Behemos, Ashtarth, Zhael, Molok, Zoniha, and Regulus (Bomberman's rival, and with the brainwashing, he is renamed Bulzeeb), and collected all the stones except the Fire Stone, which Bomberman had in his possession. Soon, Bomberman arrived and fought against Rukifellth's BHB Army, and defeated all the Astral Knights (the brainwashed Elemental Knights). Of the seven, Bulzeeb survived but was defeated by Rukifellth, and gave his power to Bomberman before Rukifellth killed him with a Gravity Sphere.
Bomberman faced Rukifellth and defeated him, but with all seven Elemental Stones brought to him, Rukifellth revealed his true plan: To let Bomberman collect the stones and bring them to him. Whether he beat the Astral Knights or lost to them, it didn't matter - either way he still got the stones. He uses them to transform into Sthertoth, Demon of the Dark. Sthertoth's appearance is a demon with claws, spikes on his shoulder, reddish brown skin, a white, slightly skull-like face, horns, and a mohawk. For all his power, Sthertoth isn't really that hard, although he does take a lot of hit points.
After Sthertoth was defeated, he tried to suck the universe into endless darkness, but Mihaele stopped him and trapped him in an orb of light, and then reunited with him, turning them back into the Angel of Light and Shadow. The angel wanted to destroy the entire universe and create it anew, but Bomberman fought him and defeated him. The angel decided that Bomberman could protect the universe and that it still had hope, and vanished, returning Lilith and Rukifellth to normal and bringing all the Elemental Knights back to life.
The Angel's gender is a subject of debate. It sounds like and is referred to by many fans as a male, but at one point, Regulus says, referring to the angel, "It looks like she brought all the Elemental Knights back to life." Also, the angel uses the pronouns "We" instead of "I".
If one fights Sthertoth without collecting all seven Elemental Stones, or after getting beaten by Mihaele's instant knockout attack, then a different cutscene will commence, in which Sthertoth takes the Elemetal Stones from Mihaele and sucks her into a black sphere, and transforms into a much bigger, more evil-looking form called Sthertoth, God of Chaos. His skin is roughly the same color, but his face is more skull-like. His shoulders and the jewel on his chest give him an undeniable similarity to the evil Digimon, Diaboromon.
In this form, only Fire Bombs and Earth Bombs can damage him. He uses many of the attacks that the Angel does, including the lasers and the electricity. After taking enough damage, he will shoot rapid fire laser beams. It is possible to avoid this attack by getting about 3/4 of the room away and then run from the front to the left when he starts firing the beams, but there is still a chance it might hit. He also uses tornados to attack which will be destroyed if hit by a Wind Bomb or if he goes into a portal to use his rapidfire laser attack.
Bomberman defeated Sthertoth, and he vanished. Lilith and Rukifellth reappeared, both back to normal. Just as they were about to leave, Sthertoth reawakened, killing Rukifellth. He destroyed Warship Noah. Bomberman and Pommy escaped, but Lilith chose to remain behind, and was killed when Warship Noah exploded. In this dark ending, the universe is left to the mercy of Sthertoth, and Lilith, Rukifellth, and the Elemental Knights are all dead (even Zoniha, in the event that one didn't beat her before fighting Sthertoth, as Mihaele most likely killed her to get her Light Stone). The credits are shown while Bomberman's ship flies through space.