After escaping from Black Ghost, the cyborgs that once rebelled against the nefarious organization are living their lives peacefully all over the world. However, when a strange dinosaur-like monster starts using sound waves to attack people and cities, Dr. Isaac Gilmore deduces that Black Ghost must be responsible and quickly scrambles to reunite the cyborgs.

Leading the group is the charismatic Joe Shimamura, also known as Cyborg 009, and joining the new resistance is the mysterious Helena, who claims to have been orphaned by the monsters attacks. Utilizing Dolphin—their submergible aircraft possessing anti-ultrasound weapons and countermeasures—the cyborgs leave to seek out the monster and Black Ghosts new hideout.

[Written by MAL Rewrite]