"Assault Lily Fruits" is set in a world where humanity faces constant threats from mysterious creatures known as the Huge. To combat these threats, young girls with special abilities, called Lilies, are trained to wield weapons known as CHARMs. The story primarily unfolds at Yurigaoka Girls' Academy, a prestigious institution dedicated to training Lilies. The narrative centers on Riri Hitotsuyanagi, a first-year student who aspires to become a strong Lily. Riri forms a partnership with Fumi Futagawa, a reserved and enigmatic girl with a troubled past. Together, they join the Garden's Garden, an elite group of Lilies tasked with protecting humanity.

The series explores the dynamics of teamwork and personal growth as Riri and Fumi navigate their partnership and relationships with other Lilies, including the confident and skilled Yuyu Shirai and the cheerful Kaede Johan Nouvel. Each character brings unique strengths and vulnerabilities, contributing to the group's collective efforts. The plot delves into the challenges of balancing combat training, personal struggles, and the emotional bonds that form between the Lilies. As the story progresses, the group faces increasingly dangerous Huge threats, testing their resolve and unity. Themes of trust, sacrifice, and resilience are woven into the narrative, highlighting the Lilies' determination to protect their world while grappling with their own fears and aspirations.