Bombmon is sent by Lilithmon & Tactimon in an attempt to take command of the Machine Empire after King Drasil was destroyed by the DigiDestined. However, MadLeomon & SkullSatamon lose the remote control they were using to control Bombmon & he goes rogue.
When the DigiDestined destroy King Drasil, Lilithmon & Tactimon jump on the chance to get rid of the Machine Empire. They create Bombmon, a mechanical bomb/rocket Digimon, to infiltrate the Royal House of Gadgetry when it is at its most vulnerable. MadLeomon & SkullSatamon are sent to launch Bombmon from Earth (allegedly to prevent QueenChessmon from discovering them on the moon), only for SkullSatamon to lose the remote.
Upon his arrival at the Machine Empire's palace, Bombmon takes a liking to QueenChessmon, despite her rebukes. Taking advice from Datamon, Bombmon decides to destroy the DigiDestined to impress her. At this point, she lets him remain on the moon under the pretense that he will dispose of them, in spite of his obnoxious personality. The DigiDestined find Bombmon's remote & try to shut him down, but he has himself rewired so it no longer affects him. Lilithmon & Tactimon will also try to reclaim Bombmon a few times, but their plans are less than successful.
Though QueenChessmon often argues with Bombmon, it is often playful & she allows him to remain at the palace. Even Kapurimon seems to be on decent terms with him despite Bombmon's efforts to woo his mother. Bombmon spends a short amount of time trying to defeat the DigiDestined & even makes some of his own Digimon, but meets with failure each time.
Quickly growing tired of Kapurimon & QueenChessmon, who will not become his queen, Bombmon somehow wrests control of the Machine Empire away from the two, declaring himself the new emperor.
When Fuujinmon & Crusadermon arrive on the moon, they set out to dispose of Bombmon. Crusadermon takes control of him with one of her love arrows. She has him attack Tokyo & battle the DigiDestined. After a long & difficult battle for the DigiDestined, Bombmon is finally destroyed by "SuperZeomon + Pyramidramon + Agunimon".