"Blossom" centers on a young girl named Hana, who lives in a secluded village surrounded by mystical cherry blossom trees that bloom year-round. The trees are said to hold the spirits of ancestors, and the villagers revere them as sacred. Hana, an orphan raised by her grandmother, discovers she has a unique connection to the blossoms—her emotions can influence their growth and color. This ability draws the attention of outsiders, including a mysterious organization seeking to harness the trees' power for their own purposes.

The narrative unfolds as Hana learns about her lineage, revealing that her mother was a guardian of the blossoms, tasked with protecting the village's spiritual balance. When the organization infiltrates the village, Hana must embrace her role as the new guardian, despite her initial reluctance. Alongside her childhood friend, Ren, a skilled archer with a protective nature, and Kaede, a wandering scholar with knowledge of ancient rituals, Hana embarks on a journey to uncover the truth about the blossoms and her mother's disappearance.

As the story progresses, Hana faces challenges that test her resolve, including confrontations with the organization's leader, who has a personal vendetta against the village. The plot delves into themes of sacrifice, legacy, and the interplay between nature and humanity. Hana's growth as a character is marked by her increasing understanding of her responsibilities and her ability to balance her emotions to maintain the blossoms' harmony. The series concludes with a climactic battle that determines the fate of the village and the blossoms, leaving Hana to make a pivotal decision about her future and the legacy she will carry forward.