In 2025, suddenly an unknown threat, called Kikou, starts to attack human beings. Numerous cities are destroyed, and humans are backed into a corner. However, they find hope. After some fragments of a Kikou are excavated, Tokyo Kikou Laboratory (Toukiken) is established. Based in the Lab, people start studying the Kikou to utilize them as their army. Humanity’s last hope is to fight fire with fire, using a Kikou to fight against the Kikou.
Nine years later, people developed a new weapon to fight the Kikou called Muttsu, which is a Kikou made using the research from the remains of a Kikou, and they are getting ready to fight with the other Kikou.
A boy, Rin Sagami and a girl, Yuzuru Midou are chosen as the Muttsu’s pilots. They bravely face their mission of carry humanity’s last hope of the future.
However, a cruel fate awaits them.