Taichi Yagami and his friends have moved on to junior high, but by that time, they have lost contact with their Digimon partners. Taichi is therefore surprised to suddenly receive a distress call summoning him to the Digital World. Once there, he learns that Digimon are living in fear of the mysterious Digimon Emperor, who is somehow suppressing their ability to Digivolve!

In the real world, Hikari Yagami and Takeru Takaishi reunite in the same fifth grade class. They share three schoolmates: Daisuke Motomiya, who reminds them both of Taichi; Miyako Inoue, a technical wizard; and Iori Hida, Miyako's neighbor. When these three children receive "D-3" Digivices, they—along with Hikari and Takeru, who still possess their own original Digivices—comprise the new generation of "Chosen Children" who must save the world once again. With the power of the Armored Digi-Eggs, they must thwart the Digimon Emperor's plans to spread his influence over the entire Digital World.