Peace has been restored to Earth... but not for long. After two short years, Sosai X announces his return by crashing into and sinking the cruise ship Queen Margaret; kidnapping one of the survivors--a four-year-old girl named Sammie Pandora, and force-growing her into GelSadora, the next general of Gallactor. The Syndicate restores its forces and begins capturing military and scientific experts, leaving the ISO no recourse but to revive its own first line of defense: the Kagaku Ninjatai. But with Condor Joe missing and presumed dead, things aren't quite the same, and even with new weapons and vehicles, the team is at a loss. Dr. Nambu compounds the problem by bringing in a new G-2, Getz the Hawk.

A surviving fragment of Sosai X mutates into Sosai Z and recruits megalomaniac Count Egobossler to create an army to conquer the world. To combat this new threat, the Science Ninja Team Gatchaman once again return with newer weapons and a new ship - the Gatchaspartan. But with the new weapons comes a heavy price: the more Ken the Eagle uses his weapon Gatchafencer as part of the Gatchaspartan's ultimate weapon, the weaker he gets as the weapon mysteriously and slowly drains his life force.