Set in the near future in Tokyo, Japan. The evil terrorist organization Galactor has declared war on the world. The group possesses more advanced technology than governments and occupies over half of the planet. Dr. Kozaburo Nambu of the International Science Organization gathers together 5 superhero ninja agents, known collectively as Gatchaman, to stop Galactor.

After trying to rescue a man on the subway tracks, two teens wake up in a room dominated by a mysterious black sphere that sends them to hunt down and kill aliens hiding on Earth.