"Digimon Frontier" is set in the Digital World, a parallel universe inhabited by digital creatures known as Digimon. The narrative centers on five children—Takuya Kanbara, Koji Minamoto, Zoe Orimoto, J.P. Shibayama, and Tommy Himi—who are chosen to become Legendary Warriors and save the Digital World from destruction. The world is under threat from Cherubimon, a corrupted Digimon who has disrupted the balance of power and unleashed chaos. The children are summoned to the Digital World by Ophanimon, a celestial Digimon, who grants them the ability to Spirit Evolve into Digimon forms using ancient Spirits.

The Spirits are divided into Human and Beast forms, each representing elemental forces such as fire, light, wind, thunder, ice, and darkness. Takuya and Koji, the primary protagonists, wield the Spirits of Flame and Light, respectively, while Zoe, J.P., and Tommy control the Spirits of Wind, Thunder, and Ice. As the story progresses, the group discovers the existence of a sixth warrior, Koichi Kimura, who wields the Spirit of Darkness. Koichi initially serves as an antagonist under Cherubimon's influence but later joins the group after overcoming his inner turmoil.

The children embark on a journey to collect the Fractal Code, the fundamental data that composes the Digital World, which has been scattered and corrupted by Cherubimon's forces. Their quest takes them through various regions of the Digital World, each guarded by powerful Digimon adversaries. Along the way, they face moral dilemmas, personal challenges, and the growing threat of Cherubimon's army, led by the ruthless Royal Knights. The group's ability to Spirit Evolve grows stronger as they learn to harness the full potential of their Spirits, eventually unlocking their Fusion and Transcendent forms.

The climax of the series involves a confrontation with Cherubimon, who is revealed to have been corrupted by the malevolent Lucemon, an ancient Digimon sealed away for his destructive power. After defeating Cherubimon, the children must face Lucemon, who seeks to destroy both the Digital and Human Worlds. The final battle tests the limits of their abilities and unity, culminating in a resolution that restores balance to the Digital World and allows the children to return home, forever changed by their experiences.