The Digital World is becoming so overpopulated that the super computer Yggdrasill who governs the Digital World can no longer handle it. Its solution is Project Ark: to wipe out most of inhabitants with the X Program. Yggdrasill chooses a very small percentage to be moved to a new Digital World and then proceeds to destroy the old one. Some Digimon who were not chosen survive anyway, and they move to the new world with a rare gift known as the X Antibody; this antibody changes their appearance and makes them more powerful, while at the same time making them immune to the X Program. No longer in control, Yggdrasill uses the Royal Knights to destroy these X-Digimon, who are outcasts in the new Digital World.
In this movie, that takes place three months after MaloMyotismon's defeat, the DigiDestined go up against Diaboromon again. Tai and Matt head back to the Internet to deal with him with Omnimon, while the younger Chosen Children go to deal with the rampage of a swarm of Kuramon (Diaboromon's Fresh form). With the help of Angemon and Angewomon (with T.K. and Kari), Omnimon was able to destroy Diaboromon again, but it turned out to be a trap, as his destruction allowed many more Kuramon to go to the Real World. Things go out of control when the Kuramon in the Real World merge to create a Mega level called Armageddemon, an alternate Mega in Diaboromon's evolutionary line. It is so powerful that neither Omnimon nor Imperialdramon were able to defeat it on their own.
Taison Maeda's Teiken High School class goes on a field trip to the Kansai region of Japan, which is where Taison is from. Taison's little brother Youkou sent a message to Taison & his older brother Fujio that their father, Monson, is sick and that they should return home to visit him. This trip back will also allow Taison to put some closure on his past regarding his friend Naoto & his ex, Haruka.
