Galactor has a spy infiltrate a passenger ship with a lot of ISO engineers onboard. He attaches a homing system to the ship and it is then blown up by firing torpedos into it.
Nambu, afraid that such a incident may happen again, sends the Science Ninja Team on a patrol. The God Phoenix dives at the spot where the ship sank and encounters crab-shaped tanks. Seizing the opportunity when the Science Ninja Team is distracted by the tanks, a submarine attaches itself to the belly of the God Phoenix. When the crab-shaped tanks are sure of this, they retreat. The Science Ninja Team doesn't trust this move, but they nevertheless go back to their base when Nambu orders them to do so. The Galactor submarine manages to easily sneak into Crescent Coral. The crew kills some engineers disguise themselves and install the homing system in the base.
The assaulted engineers are discovered and Nambu suspects that a homing system equal to that in the passenger ship has been installed. He orders Ken and Jun to find the system, and Joe and the rest to find the submarine which fires the torpedos.
Ken and Jun search the interior of the base, discover the Galactor members disguised as engineers and corner them. However, the Galactor members press a button, per Katse's instructions, which causes the submarine to blow up completely. Thus destroying the one clue as to the location of the tracking device. It's nearly impossible to search the huge base with its complicated layout.
Elsewhere, the God Phoenix is searching the bottom of the sea, but it cannot detect the submarine which hides close by.
Convinced of his victory, Katse's laughter resounds as torpedoes are launched towards Crescent Coral.
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