One year after the fight against BelialVamdemon (MaloMyotismon), the DigiDestined must face Diablomon (Diaboromon) once again. Taichi and Yamato (Matt) decide to enter the Internet with they Digimon, to fight against Diablomon again. Meanwhile the other DigiDestined and mainly the younger (Adventure 02) ones try to clear the chaos, which the masses of Kuramon spread in the real world.
While fighting the Mega Level Digimon, Angemon and Angewomon, to help Omegamon (Omnimon) in deating Diablomon for final this time, which is successful. However, this battle was a trap, with Diablomon's destruction he transforms into thousands of Kuramon and floods the real world downright.

The Kuramon collect at the Tokyo Bay and form a new even stronger Digimon: Armagemon (Armageddomon). This Digimon is even stronger than Omegamon and Imperialdramon. When Omegamon is at the end of his power, while Imperialdramon can't do anything against Armagemon, the strong wish of the DigiDestined transforms Omegamon's last power and energy into a single sword, which is grabbed by Imperialdramon and ables him to Mode Change into Imperialdramon Paladin Mode. When striking Armagemon with the "Omega Blade", he tries to escape by splitting the data of his body into millions of Kuramon once more. But Imperialdramon rises his Omega Blade and collects the energy of all people watching this fight, releasing the full power of his sword and totally anihilating Armagemon (with all Kuramon) this time.

In the light of a new morning, this movie ends and all DigiDestined are really sleepy now. The second-last scene shows a old wagon looking really familiar to the people which know it's previous purpose.