Shuji and Chise are two Hokkaido high school students barely starting a relationship with each other. Then, with no warning, a squadron of bombers from an unknown country destroy the city of Sapporo. All hope is lost when suddenly, the bombers are destroyed by a small red light floating across the sky. At this point, Shuji finds out that the one responsible for eliminating the enemy forces is Chise, who reveals herself as a cyborg engineered for mass-destruction.
Shuji and Chise are now a couple, he remains unsure of what his true feelings are. Shuji goes to the mall to get Chise a gift when tragedy rains down on their lives.
Chise reveals to Shuji that she has become the Ultimate Weapon. As the days go on she finds she is becoming more of a weapon and less herself.
Shuji and Chise take a walk on Observation Hill, in light of everything that has happened they both know they were meant to be together.
Chise leaves her military pager at home when she is on a date but the military still contacts her with the mission. When the fighting stops, Chise wants to die.
Chise decides that she dosen't really want to die because she finally has someone who she can love. At the school a earthquake nearly destroys the whole building.
Chise and Shuji clear the air and let eachother know about things they have been holding back. With the secret finally out, they decide for now to remain just classmates.
With their differences aside, Chise and Shuji realize that they can work things out a make plans to go see the sea lions and dolphins together.
Shuji's classmates are not all showing up for school, some joined the military and some have just moved on with their lives. Chise and Tetsu go on a "shopping spree".
Chise's two day adventure without any maintenance and medicine has taken a toll on her. That evening a large earth quake hits Hokkaido. Akemi tells Shuji how she feels.
Chise finds Tetsu in a dire situation. The students work hard to get the cultural festival going, however the army is a day early and needs use the school.
Chise and Shuji both take the day off of work to spend time together. Shuji learns that Chise did not show up again for work because she had not been taking her meds.
Chise takes all of her meds, resulting in her changing, the result of which could kill her or make her immortal. Shuji returns to where he and Chise started going out.
Chise does all she can to save the town's people and Shuji as impending doom closes in, but the Tsunami is too powerful. When Shuji awakes, he finds that he is alone.