A spaceship disappears, along with a device that can report and record the location of the Earth's resources.

The Science Ninja Team receives Nambu's instructions and heads towards the bottom of the sea, in the vicinity of the spot where contact with the spaceship was lost. There, prawn-shaped bulldozers leave a huge aircraft carrier located on the sea bottom to build a uranium factory. Ken stops Ryu who wants to fire a Bird Missile, and sneaks into the aircraft carrier alone.

Ken discovers the spaceship's capsule inside the aircraft carrier, but the astronauts have been taken hostage. Ken is caught then too. In reality however, the pilots have already been murdered. Showing them as if they were still alive has been a trap.

Jinpei has sneaked into the aircraft carrier following Ken on Joe's orders. He is able to rescue Ken as he is being led underground. The two of them collect the device and escape, destroying the computer in the aircraft carrier.

The commander of the carrier gets blamed by Katse, and he gets into the head of the Turtleking to hurl himself at the God Phoenix. But due to Ken's quick thinking, the God Phoenix becomes the Firebird and the flames consume everything.