Shuji (シュウジ, Shūji?), a high school student in Hokkaido, is the main character. Chise (ちせ, Chise?), a fellow student, declares her love for Shuji at the beginning of the series. However, Chise is very shy and Shuji has a bitter tongue. Neither know how to express their feelings very well, but they do indeed have them for each other.

One day, while Shuji is shopping in Sapporo, unknown bombers attack the city in broad daylight. He and his friends run for cover, but notice a fast and small flying object shoot down enemy bombers. Separated from his friends, Shuji wanders through the wreckage only to stumble upon Chise. She has metal wings and weapons apparently grafted onto her body. She tells him she has become the ultimate weapon, without her knowledge or consent. However, she is seen by the JSDF as the last hope for defending Japan from imminent invasion by unknown foreign forces for reasons that are not apparent.