Fed up with recent failures, Baron Garoga unleashes the golden terror known as King Ghidorah to wreck havoc and destruction across Earth. Meanwhile on the planet, government officials are checking up on a scientist’s recent discovery. Called the Blue-Green System, the discovery is able to take in CO2 and radioactive contaminated air and decrease the level of the contamination. As the officials praise the man’s work, Joe charges in and tries to warn them that a future terrorist attack will strike and subvert their efforts. While they argue, elsewhere in Japan the SDF is confronting King Ghidorah. Unable to coup, the jets are ripped to shreds in midair from the demon's powerful hurricane force winds.

Dismayed from his lack of progress, Joe returns home to inform the Zone Family that they need to act if they are to preserve the lab with the filtering machine. Unfortunately, by the time he returns to the laboratory the terrorists have already begun their attack. Strapping bizarre helmets to the humans called the Garoga Pack, the disguised aliens attempt to paralyze the men long enough for King Ghidrah to arrive and decimate the building and its occupants. Their plan would not come to fruition, though, as Joe and the Zone Family arrive just in time. Joe is attacked by one of the Garoga Pack helmets, while the Peace Land natives are chased outside by the murdering aliens. Once there, everyone transforms and prepares for battle. Like always, the stone grinning invaders were beaten back by the superior fighting family. Fleeing, the Zone Family transforms back and runs to help their friend and the scientist.

Fuming at his subordinates' failure, Baron Garoga orders the Dark Prism Strategy to be placed into effect. The Dark Prism is a shimmering crystal like rock that has the ability to absorb energy. Setting the trap, the aliens placed the prism on the road, where the Zone Family found it and brought it back for study. Not realizing its true purpose, Zone Angel, Fighter, and Junior use the device to trace it back to the Garoga headquarters on Earth. Once arriving there, the trio transforms to battle the gargoyle race. Shortly after defeating the aliens, King Ghidorah shows up. Answering to its master, the prism flies into the sky and begins to absorb the power of the sun and feed it to the cackling three-headed horror. Once fully powered the dragon would attack the research facility. Seeing humanity's future in the Blue-Green system, the Zone warriors transformed. Junior and Angel took the aircraft Smokey, as Hikaru grew to the giant warrior Zone Fighter. Taking to the air, the hero sought to lure the dragon away from the science building and battle it in a more appropriate area. The remaining Zone family could only watch in horror as Zone Fighter’s energy was drained from a combination of King Ghidorah’s attacks and the Dark Prism. Earth’s only hope lay in Zone Great’s hands. Using his machine, he takes control of the Great Raideki, an artificial thundercloud. Despite its use shortening his life, the old man pressed on and unleashed a wave of lighting against the three-headed monster. Knocking it down briefly, the kaiju lost its concentration over the Dark Prism, allowing the sun to seep through and recharge Zone Fighter.

In a last ditch effort, Zone Great removed the Proton crystal from the house's computer. It was the only thing that would give Zone Fighter the extra power he would need to lure King Ghidorah far out into space. Unfortunately, with removing of the crystal the family would lose their Proton Barrier and be in the future susceptible to Garoga attacks. Caring only for the life of humanity, though, Fighter used the green crystal and flew into space, followed by the winged Ghidorah.