"DNAngel" centers around Daisuke Niwa, a 14-year-old boy who discovers he carries a genetic legacy tied to the Niwa family. On his 14th birthday, Daisuke transforms into the legendary phantom thief Dark, a persona inherited from his ancestors. This transformation occurs whenever Daisuke experiences strong emotions, particularly romantic feelings toward his classmate, Risa Harada. Dark is a charming and skilled thief who steals priceless artworks, targeting pieces connected to a mysterious organization known as the Hikari family, who have a long-standing feud with the Niwa lineage.

The Hikari family, led by Krad, Dark's eternal rival, seeks to capture Dark and reclaim the stolen artworks, which hold supernatural powers. Krad, a winged being of light, is the counterpart to Dark, representing the opposing force in their centuries-old conflict. The story explores the duality between Dark and Krad, as well as the moral complexities of their actions. Daisuke struggles to balance his ordinary life with his responsibilities as Dark, often feeling overshadowed by the thief's confident and flamboyant personality.

Risa Harada and her twin sister, Riku Harada, play significant roles in the narrative. Risa is infatuated with Dark, while Riku develops feelings for Daisuke, creating a love triangle that adds emotional depth to the story. The twins' connection to the Hikari family further complicates the relationships, as their involvement becomes pivotal to the unfolding conflict.

As the series progresses, Daisuke uncovers more about the Niwa family's history, the origins of Dark and Krad, and the true purpose behind the stolen artworks. The artworks, known as the "Wings of the Night," are revealed to be fragments of a powerful artifact that could tip the balance between light and darkness. The story delves into themes of identity, legacy, and the struggle between opposing forces, as Daisuke navigates his dual existence and the challenges posed by the Hikari family.

The narrative is driven by a mix of action, romance, and mystery, with a focus on the evolving relationships between the characters. The interplay between Daisuke and Dark, as well as the tension between Dark and Krad, forms the core of the series, culminating in a climactic confrontation that resolves the central conflict while leaving room for further exploration of the characters' futures.