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 relocate to the underwater base at G-Town, where they're introduced to Kamo, an engineer who becomes crucial to their survival. When their beloved God Phoenix is destroyed in battle, the team receives the Gatchaspartan, a cutting-edge mecha designed to match Z's growing power. Ken gains access to a devastating new weapon: the Gatchafencer sword, which unlocks the Gatchaspartan's ultimate Hypershoot mode. But as the team fights back against impossible odds, they begin uncovering a terrible secret that could change everything they know about this war. Each mission pushes them closer to the truth while testing whether they can protect the world from complete annihilation.