Based on the popular Digimon manga, this is a sequel to Digimon Adventure 02: D1 Tamers. The game picks up directly where the previous one ended. After yet another ultimate battle against the evil Millenniumon, during which he revealed to the hero Ryou a terrifying secret, there was a great explosion. Ryou comes to his senses in an unknown place. The only digital monster there explains to him that the explosion send Millenniumon to the future, while Ryou ended up in the past. And now Millenniumon is trying to take control over the main computer in the Digiworld, and it is Ryou's task to stop him once and for all, and to finally find the truth about his and his archenemy's identities.

The gameplay is similar to that of the predecessors: you navigate your hero over the top-down view, descend into dungeons, fight monsters in turn-based combat, recruit them into your party, and send the new teams to fight new enemies. The battle are not isometric any more, but viewed entirely as anime-style pictures. Attacks are also depicted as animated sequences.