Long ago, human and beast Digimon were in a great war against each other. Eventually, Lucemon came down to stop the fighting and bring peace, but soon he became a cruel tyrant that believed he could only succeed in brining peace by having everyone under his complete control. Ten ancient Digimon, the Warrior Ten, sacrificed themselves to seal Lucemon in the Dark Area. However, they lived on in the Spirits. Three angel Digimon sat as the Digital Worlds rulers - Seraphimon, Ophanimon, and Cherubimo, and they also possessed the Spirits. All was peaceful for a long time.
Cherubimon, the only beast type angel, grew frustrated with Seraphimon and Ophanimon, believing they could not understand beast Digimon such as himself, they being human type Digimon. After an argument with Seraphimon and Ophanimon, he left the Forest Terminal (Seraphimon's abiding place) and was corrupted by the power of Lucemon. The evil Cherubimon turned against Seraphimon and Ophanimon, bringing a great army of Digimon to destroy the Forest Terminal.
However, Seraphimon too had an army. He sent it out to battle with Cherubimon's, but Cherubimon used the energy of all the Digimon to power up Lightning Spear - which he then threw at Seraphimon, nearly killing him. Ophanimon pleaded for Seraphimon's life, and Cherubimon agreed that he should stay sealed in a crystal, as long as Ophanimon came with him. Ophanimon watched helplessly, trapped in the Cage of Light within the Venus Rose, Cherubimon's castle, as he used the spirits to create four evil Hybrid Digimon - Grottomon, Ranamon, Mercuremon, and Arbormon. Then, Ophanimon called thousands of people to the Digital World to choose six to take the remaining Spirits, and perhaps, one day defeat Cherubimon.
But her plans went astray. Five of the Chosen Children became the possessors of the Spirits of Fire, Wind, Ice, Light, and Thunder, but the sixth was ensnared by Cherubimon, brainwashed, and then given the corrupted Spirits of Darkness, forming Duskmon. Seraphimon was deleted and scanned by Mercuremon after the Chosen Children released him. The Chosen Children gradually found their Beast Spirits and defeated Grottomon and Arbormon, but then Duskmon revealed himself. He easily defeated the Chosen Children, but as he moved to kill Takuya, as Agnimon, the Legendary Warrior of Fire, Kouji, the Chosen Child bearing the Spirits of Light lept in the way and was devolved and severely injured. Duskmon fell back in suprise when he saw Kouji, and enveloped the Chosen Children in darknesss...only Takuya escaped on the Black Trailmon to the Real World.
Takuya came back to the Digital World, and helped Kouji rescue the other Chosen Children from Ranamon and Mercuremon. The Chosen all evolved, and Mercuremon and Ranamon fled in terror. Mercuremon was not dismayed by their power though; he had other plans. He evolved to his Beast form, Sefirotmon, and sucked all the Chosen into him. Ranamon went into Sefirotmon's Water Sphere to act as it's guardian, and Duskmon went to the Darkness Sphere. Tomoki and Junpei defeated lesser guardians and escaped from Sefirotmon and Izumi defeated Ranamon, and also escaped.
Kouji found himself in the Darkness Sphere, and Duskmon read his memories in order to learn his own past. He then defeated Wolfmon in battle, and as he went to kill Kouji, Kouji used both Spirits of Light and evolved to Beowulfmon! But Beowulfmon and Duskmon were equally matched, and as they they fought, they saw what the other truly looked like. Duskmon saw Kouji...and Kouji saw a boy that looked just like him. An explosion blew them both out of Sefirotmon. Only Takuya remained...
Mercuremon toyed with him in the Steel Sphere, and led him to the Light Sphere, where Mercuremon merged himself with Seraphimon's Diig-Code, becoming Black Seraphimon. Takuya was nearly killed, but he too was able to Double Spirit Evolve thanks to Seraphimon's Digi-Tama and defeated both Black Seraphimon and then Mercuremon. With all the Spheres cleared, he was at last able to escape. But then, Sefirotmon himself fought, but eventually the Chosen defeated him too.
Meanwhile, Cherubimon gave Duskmon the corrupted Beast Spirit of Darkness, and Velgmon proceeded to defeat Beowulfmon. While Izumi, Tomoki, and Junpei learned that the Evil Hybrids had brough Ophanimon to the Venus Rose, Cherubimon's castle, Takuya joined Kouji and the combined powers of Ardhamon and Beowulfmon were able to defeat Velgmon, freeing Kouichi from Cherubimon's control. Kouji took the Spirits of Darkness.
Soon, all the Chosen Children reunited, and the ran into an avatar of Cherubimon, which defeated them all with Heaven's Judgement. However, just as he moved to finish them off, Kouji's D-Scanner gave Kouichi another D-Scanner and purified the Spirits of Darkness, and Kouichi Spirit Evolved into Löwemon. Löwmon attacked Cherubimon's avatar, Slide Evolved into Kaiser Leomon, and defeated it. The Chosen proceeded to the Venus Rose.
There, the Chosen managed to free Ophanimon, but at the cost of all the Spirits except those of Wind. Ophanimon and Cherubimon fought, and Ophanimon gave all the Chosen their Spirits and D-Scanners back, and proceeded to die in battle with Cherubimon. Her final gift was to modify the D-Scanners so Takuya and Kouji could Hyper Spirit Evolve, and they did - into Kaiser Greymon and Magna Garurumon. The two beat Cherubimon off for the time being, but he soon returned with a massive amount of Digi-Code. When Cherubimon was at last defeated, his Vaccine form stood for a while, remembering Seraphimon and Ophanimon, until it deleted. The Chosen were happy.
But it was not over. The Digi-Code Cherubimon had collected flew down to the Dark Area and into Lucemon's hands. He summoned the Royal Knights Dynasmon and Rhodo Knightmon to collect more data so he could be revived, and so they set out, encountering and - just barely - defeating the Chosen at every encounter. The ever more wakeful Lucemon demanded more and more Digi-Code faster. At last, only one area remained. The Chosen Children fought well, but Lucemon was able to send beams of light to defeat them, and the Royal Knights scanned the last remaining area of the Digital World and sent Lucemon the data. The Terror of Legends was revived.
Lucemon told the children of his plan to bring total peace, and blasted the Chosen to the moon. There, they found the Digi-Tamas of Cherubimon and Ophanimon, which hatched into Lopmon and Plotmon, and the Chosen watched the two Digimon play with Patamon, and remembered the Three Great Angels as they had once been...meanwhile, the Royal Knights reminded Lucemon of their desire and reward to rule the human world, but Lucemon commanded them to destroy the Chosen first. With this sole objective, the Royal Knights were at last defeated.
But before Kaiser Greymon and Magna Garurumon could scan the data, Lucemon flew down and used Grand Cross to knock them away, and he scanned the Digi-Code, evolving into Lucemon Falldown Mode. Lucemon Falldown Mode quickly defeated Kaiser Greymon and Magna Garurumon, and destroyed the three moons in the process. He then flew to the Dark Area and opened two portals to the Real World, but the Chosen came to stop the Demon Lord. They failed miserably, however, as Dead or Alive devolved them all and destroyed Kouichi's spirit. He gave the Spirits of Darkness to Kouji, which, basked in the Spirits of Light, became abnormally powerful and allowed Takuya and Kouji to evolve to Susanoomon, who was able to defeat Lucemon Falldown Mode.
However, two Digi-Tamas remained. A white one, and a black one. The white one burst into data and deleted the Dark Area, whilst the black one took the data of the Dark Area and evolved into Lucemon Satan Mode, with Lucemon Larva controlling him. He went to the Real World, and the Chosen Children followed, but were defeated. But in that moment, the shadows of the Warrior Ten and the Three Great Angels appeared, encouraging them and allowing them all (except the angels) to evolve once more into a more powerful Susanoomon, who dragged Lucemon Satan Mode back to the Digital World and defeated him.
Susanoomon scanned the data, but then Lucemon Larva cam from behind, stabbing him in the back - the Chosen dropped out, and all the Legendary Warriors slashed Larva apart. They then threw the Chosen into a portal into the Real World, where they were finally able to return Kouichi's spirit to his body...