The year is 2314, two years after Setsuna F. Seiei defeated the Innovator Ribbons Almark. The world is starting to move toward peace, and other people around the world are beginning to Innovate. However, an abandoned probe which went on an expedition to Jupiter 130 years ago suddenly returns to Earth, though there appears to not carry any sign of life aboard. Soon after, Earth becomes the target of dangerous aliens called the Extraterrestrial Living-metal Shapeshifters (ELS), who have the ability to assimilate Earth's technology. Celestial Being returns to combat the alien invasion with humanity's fate hanging in the balance.