MegaSeadramon is one of the Digimon Myotismon brings to the Real World, and his Digimon Analyzer profile implies that he is the Seadramon that the DigiDestined fought earlier, now digivolved into a stronger form.
On August 3, 1999, MegaSeadramon is given the task of preventing outside interference from the sea, so when Joe Kido and Takeru "T.K." Takaishi ride Ikkakumon across Tokyo Bay in an attempt to get into the city, MegaSeadramon attacks, knocking T.K. into the water. As T.K. is about to drown, Joe realizes that only he can save T.K., and his Crest of Reliability glows for the first time. Ikkakumon then digivolves to Zudomon and defeats MegaSeadramon.
Three years later, he is under the control of one of the Digimon Emperor's Dark Spirals, and traps the DigiDestined on an offshore oil platform. Cody Hida escapes in a submersible to contact Joe, who arrives with Ikkakumon and Whamon. Ikkakumon holds off MegaSeadramon while Joe and Whamon free the DigiDestined, and then Cody retrieves and activates the Digi-Egg of Reliability, digivolving Armadillomon to Submarimon. Ikkakumon and Submarimon then destroy the Dark Spiral controlling MegaSeadramon.
Even later, during BlackWarGreymon's assault on the Destiny Stones, the DigiDestined contact Ikkakumon for help protecting the sixth stone. Ikkakumon arrives with MegaSeadramon and a pod of Dolphmon, but they are unable to stop BlackWarGreymon from destroying the stone.