The enigmatic "Huge" monsters arrived all across the earth fifty years ago, posing an existential danger to humanity. Soldiers in the shape of teenage girls known as "Lilies" harness the energy "Magie" within their bodies to power weapons known as "Counter Huge ARMS" or "CHARMS" to defend against these threats. Riri Hitotsuyanagi pledged to become a Lily after being saved by a Lily two years ago while fleeing a Huge attack. She enrolls in Yurigaoka, a prominent academy for Lilies, and realizes that one of her classmates is Yuyu Shirai, the same Lily who rescued her. But, to to her surprise, the person she believed was happy turns out to be antisocial and prefers to fight.