An airplane en route to Haneda Airport is unexpectedly struck by a strange hail storm, and all of its instrumentation goes out of control. Suddenly, Mogu appears from nowhere before the plane, stunning the crew. The Kajiu quickly disappears and the storm dissipates and all returns to normal.

Later that evening, Okamoto, the plane's copilot, goes to Science Land, making his way to the Science Center located atop Godzilla Tower in hopes that an investigation of his strange experience will result in an explanation of the weird events. Entering the control room at 1:00am, he is startled when a call comes into the center since he did not tell anyone that he was coming there. Answering the call, Okamoto hears a strange voice, "I know you are there... I can answer all your questions." Okamoto becomes curious, asking who it is that's speaking. But the voice just continues, "I caused everything which you saw today. The monster which you saw is under my control, and I shall take control of the skies over Japan from this time forward. My name is Alien Miko. Ha, ha, ha!" Okamoto sits in stunned disbelief. "You can't believe it? You will see!" The call is abruptly cut off.

Several days later, radar spots a strange object over the ocean, so SDF fighter jets are sent to investigate. Making contact with the object, the pilots find the monster Mogu. An aerial chase ensues, but the planes are intercepted by a second flying monster, Gigan, who destroys several of the fighters with ease. The survivors of the squadron flee the scene and ditch their planes on a nearby island. Gigan follows the aircraft and circles the island, searching for its prey, but instead the space monster is confronted by Rodan who has arrived on the scene. Gigan lands and engages Rodan in battle on the beach. Rodan seems to be having its way in battle when Mogu arrives to double team the Earth monster. Godzilla finally comes to Rodan's aid, and quickly the two space monsters break off the attack and fly away. Almost at the same time, the squadron leader of the fighter jets gets a message over his communicator: "You are the only one left alive. My name is Alien Miko. If you can't believe it, just look above you." Looking skyward, the pilot sees the huge form of King Ghidorah gliding overhead. The alien voice continues, "King Ghidorah is my horse. Now you see who is controlling the skies over Japan. Ha, ha, ha..."

Air traffic all over the world comes to a standstill as the three space monsters rule the skies. Miko also uses his minions to destroy all of the planet's orbiting satellites. Miko issues an ultimatum to the world... turn over control of the planet to him, or he will cut off all gas, water, and electricity to the city of Tokyo as a first step in beating Earth's population into submission. As a further threat, Miko warns that if Earth does not give up soon, he will order the space monsters to attack Tokyo.

Inside the Godzilla Tower Science Center room, technicians monitor a panel of radar screens. Suddenly, the three space monsters appear on the screens, headed directly for Science Land. The invaders arrive at Godzilla Tower, mistaking the huge structure for the real Godzilla. Sizing up the tower for attack, the monsters are surprised when a resounding roar comes from behind them... the real Godzilla has come to challenge the enemies . Gigan appears poised to do battle with Godzilla but mysteriously the beast turns around, and all three leave Science Land.

Later the three space monsters appear in Tokyo and Miko announces that his servants will first take over Tokyo, New York, and Moscow, and then proceed to take control of the world. While the monsters fly over the city, tanks and fighter jets move into position and launch a strike on the creatures, but man's military weaponry has no effect on the beasts. Rodan arrives on the scene to defend the Earth, attacking Gigan. Immediately, King Ghidorah and Mogu come to Gigan's aid, but when Godzilla along with Varan show up, the three monsters fly away without fighting. Miko, a living brain, appears on television to state that he pulled the monsters back to prevent further destruction of Tokyo, blaming the military and Godzilla for the damage inflicted by his monsters. He gives a final warning: "Humans, obey Miko and you will live... otherwise you will die."

Miko then orders the three space monsters to destroying Science Land. They arrive on the scene only to find Godzilla, Rodan, and Varan ready to challenge them. The six monsters break out into battle, unfortunately for Miko he meets an untimely death during the fight, and control of the monsters is broken. The until continues until, one by one, the invaders flee to space, leaving Godzilla, Rodan, and Varan victorious.

After Godzilla vs. Hedorah 2 (ver. 2) and Godzilla vs. the Space Monster were canned, Toho went to work on a modified Godzilla vs. the Space Monster script. This time replacing Angilas, Megalon, and Majin Tuol with Rodan, Varan and Mogu. Eventually this film would get canned too, and the script would once again be adapted this time throwing out the Miko story and only keeping Godzilla, Angilas, King Ghidorah and Gigan. The film would go on to become Godzilla vs. Gigan (1972).

A interesting side note about this movie is that Gigan was able to fire a spiked ball from his right hand, a odd power that thankfully never saw the light of day.

Note, no picture of Mogu exists beyond a concept art drawing for the script. The above picture of him was done through the Toho Kingdom's interpretation of the concept drawing, using it as a model and then fleshing it out.