In 2223 AD, the migration of the human race into outer space started by the discovery of the Inflation Hall, that made faster-than-light travel possible. The Inflation Hall connects Saturn's moon Titan to outer space, and is controlled by ancient ruins, the Watcher's Nest, the relay station of the Inflation Hall, located 32 light years from the Earth. However, this important transportation system to the outer regions of space unexpectedly attracts an alien race called the Ghoul.

The 18-year-old girl Misaki, who enlisted in Seraphim — the special unit established to prevent the invasion of the Ghoul — finishes training in the solar system, and travels to Watcher's Nest, her next training post. However, a Ghoul attacks Misaki before she reaches her destination, turning her into Morph. But Divergence EVE, shouldering the cursed fate of the Designer Children, keeps on fighting. Fear changes a girl into a weapon.