Shipwrecked, Daisaku (Johnny Sokko) and Juro Minami (an agent forUnicorn) drift to an island and are captured by the BF gang. The island is in fact, a base of the B.F. gang. They happen to discover a huge robot while they are running away. Giant Robot is being constructed by Dr. Gartua who is aware of the wicked project to conquer the earth by the B.F. gang. Dr. Gartua explains that Giant Robot works by atomic energy and only obeys the person who gives the original order. When Dr. Gartua tries to destroy the robot, his lab is destroyed. From the ruins Giant Robot stands up. Daisaku speaks to it and it is decided that he is the one who can control it.

Emperor Guillotine, king of BF syndicate, plans to take back Giant Robot and to arrest Daisaku (Johhny Sokko), the only one that can give orders to the robot. He sends a huge magic metal globe called Glober to the earth. Then he orders Spider, head of the BF Japanese branch, to arrest the boy and the robot when they come to destroy it. The globe falls to the top of Mt. Makone and starts to roll down the mountain toward the town. The tank corps of the Defense Force attackit in vain and town people are thrown into confusion. Carrying a small rocket on his back, Daisaku comes flying to the town and calls Giant Robo.

Under Emperor Guillotine's orders, Dr. Over, a leading member of BF Syndicate, comes to the earth with a fossil of a devilish space plant called Satan Rose. He kidnaps Yasui, an old botantist. In the underground laboratory Over tells him to bring the seed of the plant back to life. As Yasui refuses, the doctor performs an operation on his brains. Now as Over's slave, Yasui obeys his orders. The fossil breaks into two and a small black bud starts to grow. Put in a building and destroys it. People are struck with terror and run about helter-skelter.

Emperor Guillotine sends Dr. Over and Ligon, a new weapon in the shape of a pyramid, to the earth. By operating Ligon, Over destroys oil fields in Araia one after another. The price of oil soars in all countries and the world economy is thrown into confusion. Then the doctor tells Hishino, a Japanese oil engineer in the Arabian Desert to help him. Hishino refuses, and he is imprisoned in Ligon together with Arabian members of Unicorn Organization. Suspecting that all the trouble was caused by BF Syndicate, the head of the Japanese Branch of Unicorn Organization sends two members -- Minami and Mitsuko, Hishino's sister -- to Arabia. On the way their plane explodes, but they are rescued by Daisaku (Johnny Sokko) and Giant Robo who have been following the plane.

A strange huge plant which has appeared suddenly in Sagami Lake sucks in all the water including a sailing boat and a man in it. Azuma, head of the Japanese Branch of Unicorn Organization, thinks that it must be Satan Rose, a space plant brought to the earth by Dr. Over. He sends Daisaku (Johnny Sokko) and Minami to the house of Yasui, an old authority on the plant. Meanwhile Over tells Red Cobra, new head of the Japanese Branch of the syndicate, to kill Yasui before he gives information about the plant to Unicorn members.

Dr. Over makes Ligon swallow a train near Lake Biwa to kidnap Suzuki, one of the passengers and head of the Kyoto Branch of Unicorn Organization. In the headquarters of BF Syndicate in the bottom of lake, Suzuki sees Over and Black Dia, new head of the Japanese Branch of the Syndicate. Azuma thinks that Over has killed Suzuki, for he is in charge of the conference of Unicorn leaders of the world which is going to be held in Kyoto. Under Azuma's orders, Daisaku (Johnny Sokko) and Minami go to Kyoto carrying the important papers concerning the conference. Over and Black Dia try to steal the papers, but they fail. Over changes Suzuki into a cyborg by performing an operation on him.