You're fighting the same enemy twice. First you killed Leader X, thought it was over, felt the weight lift. Now a fragment of him is crawling back, mutating into something worse, and you realize victory was never the finish line. The team is trapped in an underwater base with a new commander and new engineers, running on fumes against an enemy that refuses to stay dead. This is what happens when you win but the war doesn't end.
A fragment of the defeated Leader X mutates into Z, a new threat determined to obliterate Earth and the Science Ninja Team alongside it. Count Egobossler and his forces stand ready to finally crush humanity's defenders. With Anderson gone and Dr. Nambu now leading the ISO, Ken and his team are stationed at the underwater base of G-Town, where they meet the engineer Kamo. When the New God Phoenix is destroyed early on, the team receives the Gatchaspartan as its new mecha. Ken wields the Gatchafencer sword, and only he can trigger the ship's special Hypershoot mode. Yet repeated use of that power exposes him to radiation that slowly wears away his life, while Z prepares to wipe out the planet with an antimatter asteroid code-named Poison Apple.
