"Assault Lily Bouquet" is set in a near-future world where humanity faces a constant threat from mysterious creatures known as the Huge. These monstrous entities emerge from portals and wreak havoc, prompting the creation of specialized weapons called CHARMs (Counter Huge Arms) and the formation of Lilies, young women trained to wield these weapons in combat. The story primarily unfolds at Yurigaoka Girls' Academy, a prestigious institution where Lilies are trained to protect humanity.

The narrative centers on Riri Hitotsuyanagi, a first-year student who transfers to Yurigaoka with the goal of becoming a strong Lily. Riri is determined to follow in the footsteps of her idol, Yuyu Shirai, a legendary Lily known for her bravery and skill. Upon arriving at the academy, Riri is assigned to the Garden of Eden dormitory, where she meets and forms bonds with other Lilies, including the reserved but highly skilled Yuyu Shirai herself. The two quickly develop a close partnership, with Riri aspiring to fight alongside Yuyu as her "partner" in battle.

As the story progresses, Riri and her classmates face various challenges, both in their training and in combat against the Huge. The series explores the dynamics of teamwork, trust, and personal growth as the Lilies learn to synchronize their abilities and emotions to maximize their combat effectiveness. A key element of the narrative is the concept of the "Magie," a unique energy that Lilies generate through their bonds with one another, which powers their CHARMs and enhances their abilities in battle.

The plot delves into the personal struggles and motivations of the main characters, particularly Riri and Yuyu. Riri's determination to prove herself and her unwavering admiration for Yuyu drive much of her character development, while Yuyu grapples with her own insecurities and the weight of her reputation as a legendary Lily. The series also introduces other members of the Garden of Eden dormitory, each with distinct personalities and backgrounds, contributing to the group's dynamics and the overarching narrative.

As the Lilies face increasingly powerful Huge, the stakes rise, and the story explores themes of sacrifice, resilience, and the importance of human connections. The series balances action-packed battles with moments of introspection and camaraderie, creating a narrative that emphasizes both the physical and emotional challenges of being a Lily. Through its exploration of friendship, duty, and the fight for survival, "Assault Lily Bouquet" presents a story that intertwines personal growth with the larger struggle to protect humanity.