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.

One peaceful day on Earth, two remnants of Frieza's army named Sorbet and Tagoma arrive searching for the Dragon Balls with the aim of reviving Frieza. They succeed, and Frieza subsequently seeks revenge on the Saiyans.