An enormous dragon-shaped warship decimates a city with plasma beams and giant robotic arms. Its target is the Mantel Plan, a network unifying the world's energy resources. As the sinister ship heads for its next target a team of specialists rise to the rescue: the Gatchaman. Piloting their ship, the Phoenix, the Gatchaman launch a counterattack. Once inside the enemy ship they come face to face with the Galactor's entire army of assassins.

The Gatchaman are in trouble and receive help from a mysterious group known as Red Impulse. While cruising near a strange island a submarine is vaporized by a large blast. Summoned to avenge the attack the Gatchaman Group comes upon the secret undersea headquarters of the alien Galactor. In a fierce air and undersea battle the Gatchaman struggle against the Galactor's Jupiter Death Brigade and the evil Black Bird Battalion. Battered by combat, the Gatchaman appear to be on the brink of defeat when, out of the sky, a new force appears led by a mysterious warrior in red.

The Gatchaman have to confront Berg Katse in a final battle to save the earth. The huge mechanical devices installed at each of the Galactor's bases are infiltrating the Earth's interior, disrupting weather patterns and transforming the Earth's landscape into an environment hostile to the human race. In the midst of these disasters Joe is beginning to regain his childhood memories and must deal with the realization that he may be descended from the blood of his enemies. Joe decides to use his knowledge of the Galactor society to help save the human race. Joe single-handedly infiltrates the Galactor headquarters and manages to transmit its coordinates to the Gatchaman moments before he is captured by Solaris and his henchman.

Meanwhile the Gatchaman group teams up with Red Impulse to attack the Galactor's home base – it's a brutal fight to the death in which both the Gatchaman and the Red Impulse will pay the ultimate price. In the end-credits, it turns out that the Gatchaman team survived thanks to a miracle.