The game is based on the manga series Digimon, in which children can travel to a digital world and help good digital monsters to defeat evil ones. In this game, the two heroes, Ryou and Ken, are summoned to the Digiworld to fight against the archenemy Millenniumon and his side-kick Diablomon. Upon defeating the two evil monsters once again, the heroes realize that Millenniumon has taken a different shape and is reborn to conquer the Digiworld anew. Now you must recruit digital monsters and lead them into the ultimate battle.

The gameplay follows traditional Digimon outlines: you descend into dungeons and have your monster friends fight other monsters in turn-based combat. Upon returning to the town, you can make those monsters participate in future battles. Unlike the two previous Digimon Adventure games, Anode and Cathode Tamers, you cannot move over the battle field.