Long ago, a group of ten Digimon sacrificed themselves to defeat an ultimate evil that threatened the Digital World. These Ancient Warriors created artifacts from their data, the twenty "Spirits" (ten Beast spirits and ten Human spirits, one of each for each element), before leaving the Digital World in the care of the three Celestial Digimon. However, one of the three, Cherubimon begins a reign of terror. To counter this, the Celestial Digimon Ophanimon summons five children from the human world into the Digital World via the train-like Trailmon. There, these five Digi-Destined find their respective Human Spirits and "Spirit Evolve" into Digimon, the Legendary Warriors. However, while finding their respective Beast Spirits, the five find themselves hunted by five other Legendary Warriors that serve Cherubimon (for five of these spirits were given to the care of Cherubimon before his corruption).
After they defeat four of the them (JP destroys one, another loses his Beast Spirit to Koji and is destroyed by Duskmon for being useless, Zoe destroys another and Takuya gets the last one), Koji Minamoto discovers that Duskmon, the fifth evil Legendary Warrior, is really his twin brother Koichi Kimura. With Takuya Kanbara's help, Koji is able to free his brother, and Kouichi restores the Spirits of Darkness to their true forms and joins the team as the true Warrior of Darkness, Löwemon. After they defeat Cherubimon who is killed by Takuya as EmperorGreymon, the DigiDestined learn that the true mastermind was the very evil the Ancient Warriors sealed away within the Digital World's core, Lucemon. So now the six DigiDestined must try to defeat the two Royal Knights who were sent by Lucemon to scan all of the Digital world's data to complete his rebirth. Ultimately Takuya and Koji succeed in destroying the Knights, but not before they destroy and scan the whole world, along with its three moons, also not before they free Lucemon (who scans the Royal Knights after the DigiDestined destroy them). At this point, after killing Koichi (who sacrificed himself to save the others' spirits), Lucemon opens a portal to the real world: a portal that leads to the underground train station in which the DigiDestined were brought. Forming the ultimate digimon Susanoomon by combining all the spirits in Takuya and Koji, Lucemon is defeated and scanned. However, all of his evil transforms in another form of Lucemon, one of pure evil, which tries to go to the real world. Having almost giving up, the spirits of the ten Legendary Warriors come to life, along with the spirits of Ophanimon, Cherubimon and Seraphimon, giving the kids new hope. Together, they all form a seemingly more powerful Susanoomon, and defeat Lucemon once and for all, giving the Digital World its data back, ultimately restoring its true form. The children go back to the real world, to exact time in which they left it. They find Koichi, who they discover was only in the Digital World for having been in a coma for falling down a flight of stairs. He then wakes up when Koji arrives, leading everyone into living happily ever after, having the events of the Digital World change them forever.