A huge whale keeps attacking harbours. While investigating a group of whales, the Science Ninja Team discovers a huge whale heading for this group. The huge whales fires a rocket aiming for the God Phoenix and flees, pushing aside the other whales. In reality, it's a Galactor submarine camouflaged as a whale.

They want to follow the huge whale submarine, but, in order to save a young whale under attack by orcas, the G4 flies away. During all this, the submarine gets away. Nambu reproves them because of their squeamishness and puts a transmitter on the small whale so that he can help in the search for the big whale.

The God Phoenix goes to the Arctic Circle, following the small whale. In order to search for the base, Ken and Joe leave the God Phoenix and encounter two men who introduce themselves as forest-keepers, but are then attacked from behind. Ken is baffled. Joe says that this is Galactor's trick and that his parents got murdered by the very same trick.

The Science Ninja Team discovers the base and sneaks into it. They learn that a group of submarines is about to leave and attack the harbours in the world. They install explosives in the base and in the submarines.

But, in order to help the little whale who ended up in the base, Jinpei dives with him into the sea. The Science Ninja Team can't stop the operation at this point, and escapes leaving Jinpei. But after the explosion of the base and the submarines, they are contacted by Jinpei, saying that he was saved by the small whale, and everybody is very relieved.