The story takes place on an island, where a Fractale System is beginning to collapse. One day, Clain finds an injured girl called Phryne under a cliff. She disappears leaving a pendant. Clain sets out for a journey with the girl-shaped avatar Nessa to look for Phryne and discovers the secret of the Fractale System.

Short specials included on the BD/DVD volumes of Freezing Vibration.

2041, Earth. After being pulled into the planet's atmosphere, the fall of the Freeport Space Station has led to the Great Cataclysm—an event that devastated the Earth's environment. Left as a polluted wasteland, survivors go to war with their fellows to guarantee themselves resources; in the end, these scrimmages have erased the whole existence of humanity. Coincidentally, life still exists on a moon base. Although it is supposedly meant as an immigration outpost for the mission to explore Mars, it is soon turned into a city, both regulating and allowing its citizens to flourish. The lunar base, officially named The City of Eden, holds the hope of fully colonizing the moon. Takeru, one of many citizens of Eden in the year 2267, participates in Tube Races between gangs and groups using hovercraft-like vehicles. Due to causing an accident in one of his races, Takeru is sentenced to complete volunteer work outside the city. While clearing his punishment, Takeru stumbles upon remains that may unravel the truth about Earth and Eden's genesis.

Ever since the 10th NOVA clash, the Chevalier had concluded that the NOVA have been appearing at a steadier rate and they are losing more Pandoras than they can produce. Their solution is the E-Pandora Project which involves normal humans being given the power to become Pandoras. Inviting Pandora from around the world to their Alaskan base witness the unveiling of their new project, Satellizer, Kazuya and Rana are among those who have been summoned. However, as time goes the E-Pandora Project starts to become fishier and the Pandoras start to grow more and more concerned...