Possessing outstanding reflexes, Taiki, a soft-hearted person who can't say no when it comes to being asked a favor, has participated in various sports clubs. One day, after finishing basketball practice, Taiki hears a mysterious melody. When he listens carefully to it, he hears someone breathing feebly, who is about to die at any moment, crying out for help.
Later, when Shoutmon's heart responds to Taiki's voice, a mysterious, legendary device called the Digimon Xros Loader appears in front of him. Taiki was chosen as a "General" to control it. Shoutmon's fading melody is absorbed by the Xros Loader and then Taiki, along with his childhood friend, Akari and fellow classmate, Zenjirou, are dragged into another world, the Digital World. Once there, Taiki immediately sees Digimon fighting. In the Digital World, the Bagra Empire, who are aiming for hegemony, continues to advance aggressively, so Shoutmon and his friends' peaceful village has been vulnerable to all-out attacks from the Bagra Army up until now. Despite Ballistamon fighting bravely with his superhuman strength, they appear to have an overwhelming disadvantage. Revived after being inside Taiki's Xros Loader, Shoutmon emerges from it. Shoutmon fights desperately along with his friends from the village. However, the Bagra Army drive them into a corner. Unable to let the crisis just slip past, Taiki immediately protects Shoutmon. At that moment, the Xros Loader responds and at Taiki's command, Shoutmon and Ballistamon unite.
That was the moment in which a "DigiXros", a form of fusion special even in the Digital World, took place. By gaining this new power, Taiki, Shoutmon and the others drive away the Bagra Army. Kiriha, a youth in the same grade as Taiki who leads Greymon and the others, later becomes a powerful rival to Taiki and furthermore, they are watched over by a mysterious beautiful girl named Nene. Taiki and Shoutmon form an army using the Xros Loader and battle against the powerful Bagra Empire, who plan on taking over the Digital World, gradually gaining more supporting allies such as Dorulumon.
Continuing to fight alongside Shoutmon, does Taiki wish to become king of the Digital World? Or return it to peace? Now, an epic war in the Digital World begins.