Oceangoing ships from the ISO keep disappearing. It always happens in the vicinity of a place called "Cemetery of the Sea". Director Anderson and Nambu ask the Science Ninja Team to go to a base on the ocean floor which is most likely to be struck next.
The Science Ninja Team gets Nambu's message and takes the God Phoenix towards the base at the bottom of the sea. Then they encounter a mysterious submarine, which leads them to the Cemetery of the Sea, where they see countless sunken ships.
But when Joe says that all the ships are actually battleships, Ken gets suspicious and has the God Phoenix surface. There's fog everywhere on the surface. From the middle of the fog, a ghost fleet attacks them, but the Science Ninja Team guess correctly that the fog is man-made. They destroy the device creating the fog, but from the ghost fleet appear countless disks which attack them using light rays. The Science Ninja Team has to fight a hard battle.
Just when all the missiles are used up and they don't know what to do, three red planes appear and shoot down the enemy machines using superior flying techniques. The commander of the fighter plane unit introduces himself to the baffled Science Ninja Team as "Red Impulse". He then flies away, leaving the words "We'll meet again" behind.
