While at summer camp, seven kids come across seven Digivices and are transported to a strange digital world. In this new world they make friends with creatures that call themselves Digimon who were born to defend their world from various evil forces.

With most of the original characters now in junior high school, the Digital World was supposedly secure and peaceful. However, a new evil has appeared in the form of the Digimon Emperor, a human just like the DigiDestined, who has been enslaving all Digimon. Three new children are chosen to save the Digital World and, along with T.K. and Kari, make up the new generation of DigiDestined.

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.