Two years after the battle against Eosmon, Davis Motomiya, Ken Ichijouji, Yolei Inoue, Cody Hida, T.K. Takaishi, and Kari Kamiya meet a boy named Rui Owada, who is found with a depowered Digivice and claims to be the first Digidestined ever. In addition, a Digimon named Ukkomon appears in the real world, who wants every person in the world to have their own Digimon partner.

A.D. 2089 - 80 years have passed since Space War I changed the lives of both human and Zentraedi races. Both races are at peace on Earth when a new alien race called the "Marduk" appear within the Solar System. While covering the first battle between the U.N. Spacy and the Marduk fleet, SNN rookie reporter Hibiki Kanzaki discovers Ishtar, an "Emulator" that enhances the Marduk's combat abilities through singing. Hibiki brings Ishtar to Earth to teach her the values of life and culture. Together with ace Valkyrie pilot Silvie Gena, Hibiki and Ishtar must find a way to save Earth from total destruction at the hands of the Marduk leader Ingues.

The fight has moved on to the next stage. A new plan is in motion... A new battle among the strongest warriors gathered across space and time has now begun!