MegaSeadramon first showed up under control of one of the Digimon Emperor's Dark Spirals, cornering the DigiDestined on an offshore oil platform. Cody managed to escape in a submersible and reach Joe, who showed up with Ikkakumon and Whamon. While Ikkakumon kept MegaSeadramon busy, Joe and Whamon got the trapped DigiDestined to safety. Cody then grabbed the Digi-Egg of Reliability and used it to digivolve Armadillomon into Submarimon. Between the two of them, Ikkakumon and Submarimon destroyed the Dark Spiral controlling MegaSeadramon.
Later, when BlackWarGreymon started tearing through the Destiny Stones, the DigiDestined called on Ikkakumon to help defend the sixth one. Ikkakumon brought MegaSeadramon and a whole pod of Dolphmon to the fight, but even with the backup, they couldn't stop BlackWarGreymon from smashing the stone.
Content compiled by AnimeList.moe from publicly available sources.
