Century Battles takes off two months after the events of Revenge of Diaboromon.
Two months have passed since the battle between Imperialdramon Dragon Mode and Armageddemon. The barrier between both the Digital and Real World has been broken. The United Nations have just established an international treaty granting Digimon the same rights as humans. In order to reinforce these rights, the Digital Monster Official Relations Board (DMORB) is, in turn, founded by the UN. But within the organization's body, mysterious activities have taken place. And are having a negative impact on the Digimon population. The DigiDestined, along with a select few children, must heed destiny's call again and thwart the organization...before the entire Digital Monster populace is wiped out...
As the events unfold, the twelve kids' lives will intertwine again. Then the lives of a chosen six, heirs to carry out the DigiDestined legacy, will be thrown into battle in unimaginable ways. The Calamity will ensue. The battle will begin...
- Taichi "Tai" Kamiya
- Yamato "Matt" Ishida
- Sora Takenouchi
- Koushiro "Izzy" Izumi
- Mimi Tachikawa
- Joe Kido
- Takeru "T.K." Takaishi
- Kari Kamiya
- Davis Motomiya
- Yolei Inoue
- Cody Hida
- Ken Ichijouji
- Christopher R. Martin: An enigmatic American DigiDestined, he is often referred to as "R. Martin" (a reference to R. Martin Klein, Gomamon's voice actor) or simply "Martin" who, like Willis before him, communicates with the Japanese DigiDestined. Providing leaked information regarding the DMORB. He bears the "Paradoxical Crest"—the Crest of Faith. His relationship with his parents is best described as unsteady. His loyal Digimon partner is Dorumon.
- Benedict 'Benny Blue' Rambaldi: One of the older DigiDestined around the world (at age 20), he hails from Canada. He is a headstrong Interpol officer who confirms his suspicions on the DMORB and has conducted an investigation. Benedict (often referred to as his nickname 'Benny Blue', or just 'Blue') is hot-blooded and impatient, refusing to rest until he accomplishes whatever task he is given. Possessing a calmer outlook, his partner Kotemon nonetheless shares the same sense of justice.
- Rudolf Leichardt: Currently one of the youngest DigiDestined, Rudolf is a kind-hearted, well-mannered English boy raised by the proud and currently troubled Leichardt House. Noticing that his father and current head of the House is facing financial trouble with the DMORB, he and his partner Bearmon find a way to ease his burden. The solution—the destruction of the Digital Monster Official Relations Board.
- Elizabeth 'Lizzy' Munroe: The daughter of the Mayor of a local South African town. Elizabeth may be compassionate and caring, but she emerges into a determined young girl in the right situation. After noticing the DMORB's activities at her hometown, she decides to look further into the matter. She then discovers a huge reduction in the town's water supply due to a dam constructed by the DMORB. Refusing to watch her fellow townspeople suffer, she and her partner Koemon begin to search for clues and help regarding the DMORB.
- Lucas and Lucia Johansen: Hailing from Sweden, Lucas and Lucia are identical twins with different personalities. Lucas is adventurous and well-meaning. Lucia is the more studious and aware twin. Nonetheless, they care for one another and love each other. In a tragic turn of events, Lucas was taken away by the DMORB. His partner Dracmon is left without no choice but to oblige with their bidding. Determined to save her brother, Lucia and her Ryudamon embark on their quest to crush that one organization.
- Succubimon: A Mega-level Witch Digimon of the Virus attribute. Succubimon is an individual with a flirtatious air, always looking for thrills. She has an affinity for toying with her opponents and often uses sexual innuendos and alluring gestures to rouse their attention. Succubimon's build is that of a woman with a very slim figure with a massive bust and sharp fingernails and dressed in a business suit, similar to Mature and Vice from The King of Fighters. Her attack is 'Noxious Love', which shoots out a heart-shape of energy and can have disastrous effects on the opponents such as sickness, physical pain or slowly corrupting a Digimon's data. Her name comes from the mythological succubus.
- Dantiamon/Tandemon: A Mega-level Humanoid Digimon of the Data attribute. Dantiamon/Tandemon is an extremely powerful Digimon with an ego to boot. He is a very calm and very ruthless man, not stopping until his opponents are completely obliterated. However he surprisingly show signs of a good heart, especially when Lucas Johansen or R. Martin is near. His relationship with the DMORB is never fully elaborated, as are those with Lucas or Martin, but is surely significant. Whether or not he poses a threat to the Digital World is still unclear. But he is determined to destroy the real world—to "take his revenge" against 'those four'. He bears the appearance of a cyborg with the Yin Yang symbol for eyes and a giant blade-whip behind his back as a weapon, similar to that of Ivy from the Soul series.