The conserved brains of famous doctors keep getting stolen. A monster also steals the brain of Dr. Yamashina, an expert in robot engineering. The Science Ninja Team follows it, but lets it get away.
But Nambu gets a hold of one of the tentacles from the monster. Analysis shows that the monster is the low life form Bem from space. Nambu fears that if Galactor's scientific powers can control space life forms, they may be able to revive the dead brains.
At a scientific exhibition, Dr. Yamashina's creation, the X1 robot X1, is planned to be revealed. In order to achieve that, Director Anderson requests protection for it. At the exhibition, Bem appears, unites with X1 and escapes. The God Phoenix pursues it, and discovers Bem again at the spot where it lost sight of him before.
Galactor has Bem and the robot unite. With the brain energy of the doctors Superbem is completed. Ken has it followed by the God Phoenix and sneaks into the base himself.
In the base, the commander guiding Bem notices that a brain don't have enough output. In reality, the stolen brain of Dr. Yamasina is an imitation placed by Nambu on purpose. Ken sneaks in there and destroys the energy source for Bem. His plan having failed, Katse orders the self-destruction of Bem. Bem and the base explode together and the God Phoenix, uniting with the G1, escapes the explosion using the Firebird.