"D.C. ~Da Capo~" is set on Hatsunejima, a fictional island where cherry blossoms bloom year-round due to a magical tree. The story centers on Asakura Junichi, a high school student living with his stepsister, Nemu, and their grandmother. Junichi and Nemu share a close bond, but their relationship becomes complicated when Sakura Yoshino, a girl who claims to be Junichi's cousin, arrives on the island. Sakura reveals that she is a descendant of the magical tree and possesses the ability to grant wishes, though at a cost.

As the narrative unfolds, Junichi navigates his relationships with Nemu, Sakura, and other classmates, including the cheerful Kotori Shirakawa, the reserved Moe Mizukoshi, and the enigmatic Miharu Amakase. The story explores themes of love, friendship, and the consequences of wishes, as Junichi becomes entangled in the lives of those around him. The magical tree's influence looms over the island, creating a sense of mystery and tension as characters grapple with their desires and the unintended outcomes of their choices.

The series blends slice-of-life elements with supernatural undertones, focusing on the emotional dynamics between characters. Junichi's interactions with the female cast drive much of the plot, with each character's backstory and personal struggles adding depth to the narrative. The story gradually reveals the true nature of the magical tree and its connection to the island's inhabitants, culminating in a resolution that ties together the themes of love, sacrifice, and the passage of time. The series is characterized by its gentle pacing, emotional moments, and exploration of the complexities of human relationships within a fantastical setting.