After a strategic maneuver, Senkuu Ishigami's team stalls Dr. Xeno's more scientifically advanced forces. A ceasefire between the two factions allows for the establishment of Corn City in North America, a hope for a future thriving population. Meanwhile, Senkuu and some of his teammates rush toward the Amazon in South America—the epicenter of the petrification beam's impact—to create Superalloy City and progress their spaceship project. With dangerous enemies still pursuing Senkuu and his companions, it is a race against time to reach the heart of the dense Amazon. As unexpected allies and scientific creations further fuel this leg of their journey, Senkuu is closer than ever to finally uncovering the mystery behind the petrification phenomenon.

While the mission to exorcise Jin "Jiji" Enjouji's family home is underway, things are not going as expected. Momo Ayase narrowly evades an attempted abduction while Ken "Okarun" Takakura and Jiji are ambushed by the Kitou family—the unsettling landlords of the cursed estate. The trio's efforts threaten the foundation of this enigmatic town shrouded in legends and mysteries. As Momo, Okarun, and Jiji are drawn deeper into the maze of folklore and supernatural entities, they must each utilize their unique powers if they want to survive and unravel the secrets of the uncanny town.

2150 AD. The battle against the silicon-based Festums from outer space reaches a new phase. Fragments of the North Pole Mir were scattered throughout the world. Eventually, they began to act on their own as independent Mirs. Most hated humanity and attacked them, but some chose to coexist with mankind. Some with the same way of thinking existed within the human race, as well: those who were both human and Festum. They added to the chaos of the battle and brought about even more hatred.

Continuation of Soukyuu no Fafner: Dead Aggressor - Exodus.