Takuya, Koji, JP, Zoe and Tommy are traveling with a trolley-like Digimon through an endless desert. But while Takuya and Koji argue again a whole island suddenly falls out of the blue down to earth. When the children wake up, they noted that they were separated. Takuya, Tommy and J.P. were taken by Kotemon and the H-Hybrid Digimon and Koji and Zoe meets on Bearmon and a number of B-Hybrid Digimon.

When the children come together again, both groups are influenced differently. While some of them are on the side of the H-Hybrids the other one are standing on the side of the B-Hybrid Digimon and they can't really realize in what great danger they are 'cause the two groups of Digimon are in the middle of a bid war against each other. Now the kids decide to stop this fight. Right at the beginning Takuya is fighting for the H-Hybrid Digimon as Agunimon and Koji as KendoGarurumon for the B-Hybrids while Tommy, Zoe and JP are exploring a cave with a mysterious puzzle inside which has to be solved in order to reveal one of the biggest secrets of this world.

Who is responsible for this war and what is it for a secret which will be revealed if the puzzle is cmopleted? Can H-Hybdrids and B-Hybrids live together in peace ever again?