Most Bomberman games have a secret boss, usually one on a hidden level, or else an alternate final boss.
Bomberman 64
Altair is the false final boss of Bomberman64. However, if a player collects 100 Gold Cards and then defeats Altair, a cutscene will commence in which Sirius kills Altair and reveals that he is the bad guy. This will unlock the sixth stage, Rainbow Palace. At the end of Rainbow Palace, Bomberman must fight Sirius. Halfway through the battle, Regulus enters to fight alongside Bomberman, and in the end Sirius was destroyed.
Bomberman 64: The Second Attack
Rather than a hidden level, the secret boss of The Second Attack is an alternate final boss: Sthertoth's final form. If a player defeats Mihaele, and therefore has all seven Elemental Stones, then after defeating Sthertoth (Demon of the Dark), Mihaele will combine with Sthertoth to form the Angel of Light and Shadow. However, if a player enters Warship Noah and is missing the Light Stone and/or the Shadow Stone, or if Bomberman is hit with Mihaele's instant knockout (Bludgeoning Blow), then after Bomberman defeats Sthertoth, he will trap Mihaele and transform into Sthertoth: God of Chaos. This battle is harder than the angel, and once defeated, Sthertoth will seem to die, but return, killing Rukifellth, and destroy Warship Noah. Bomberman and Pommy escape but Lilith is killed in the explosion, as she chooses to remain behind, and presumably Sthertoth has his way with the universe from here.
Bomberman Hero
Bagular is the false final boss of Bomberman Hero, as he is Bomberman's main enemy. However, the one who engineered Bagular's revival and Princess Millian's kidnapping is really Evil Bomber. To get to Evil Bomber, Bomberman must collect all the Adok Bombs and get Gold on every level (beat each boss within the target time, and get a certain number of points for all the other levels). Once he does this, Gossick Star will appear. After two stages, Bomberman will fight Evil Bomber. The fight is similar to Baruda, except he has more deadly attacks. After eight hits, Evil Bomber is destroyed. His death scene is identical to Natia's.