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.

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!

U.C. 0083 - Three years after the end of the catastrophic One Year War, peace on Earth and the colonies is shattered by the presence of the Delaz Fleet, a rogue Zeon military group loyal to the ideals of the late dictator Gihren Zabi. Delaz Fleet`s ace pilot Anavel Gato, once hailed as "The Nightmare of Solomon", infiltrates the Federation`s Torrington base in Australia and steals the nuclear-armed Gundam GP02A "Physalis" prototype. Rookie pilot Kou Uraki - with the aid of Anaheim Electronics engineer Nina Purpleton and the crew of the carrier Albion - pilots the Gundam GP01 "Zephyranthes" prototype in an attempt to recover the stolen Gundam unit and prevent another war from breaking out.