"Sakura Capsule" centers on a near-future world where advanced biotechnology has led to the creation of "Capsules," small devices capable of storing and transferring memories, emotions, and skills. The story unfolds in a society where these Capsules are widely used, blurring the lines between individuality and shared experiences. The protagonist, Aoi Hoshino, is a high school student who stumbles upon a mysterious Capsule containing fragmented memories of an unknown person. As Aoi begins to experience these memories, she becomes entangled in a web of secrets involving a clandestine organization experimenting with memory manipulation.

Aoi's journey leads her to uncover the truth about the Capsule's origin, which is linked to a young scientist named Rina Kagami, who disappeared years earlier under suspicious circumstances. Rina's research on Capsules had revolutionary potential but was deemed too dangerous by those in power. As Aoi delves deeper, she encounters a group of individuals who have also been affected by Capsules, each with their own motivations and connections to Rina's work. Among them is Kaito Shiraishi, a former colleague of Rina's who harbors guilt over her disappearance, and Yuna Tachibana, a hacker determined to expose the unethical practices of the organization behind the Capsules.

The narrative explores themes of identity, memory, and the ethical implications of technology. Aoi's investigation reveals that the Capsules are being used to manipulate people's lives, erasing or altering memories to serve the interests of powerful entities. The story builds toward a confrontation with the organization, as Aoi and her allies work to dismantle its operations and uncover the full extent of Rina's research. The series balances its sci-fi elements with personal stakes, as Aoi grapples with the impact of the Capsules on her own life and relationships, ultimately questioning what it means to retain one's sense of self in a world where memories can be traded and rewritten.