The three head for home, leaving behind an empty lake bed. Goro (played by Katsuhiko Sasaki) happens to be a scientist who is working on a new robot. He and the others enter the apartment to find it a total wreck. (It is at this point, in the MST3K version, that Crow yells, "OhmyGod the humidifier committed SUICIDE! Sorry, but I thought that was funny and needed pointing out!)

Two thugs appear out of the darkness and hit Goro and Roku over the head; one of them struggles briefly with Jinkawa before hitting him over the head too! Jinkawa gives chase to the two thugs in his little car but loses them when one of them throws a firebomb his way. Roku has discovered a strange looking substance next to the robot...like red sand? Goro takes a look both at the sand and at the button that Jinkawa had pulled off the man's jacket in the struggle and concluded that either they were from Easter Island or from the bottom of the sea bed. Goro shrugs and completes his robot which he gives the name Jet Jaguar (the robot of every D.C. bureaucrat's dream!)

The bad guys kidnap Roku while he is on his motor bike. They take the boy to the apartment where they stun Goro and Jinkawa. They then take control of the robot. The Seatopian leader (a white guy dressed in a white towel and looking like he's had a VERY bad day!) sends their god Megalon to wreak havoc on the Earth people for having messed up Seatopia with nuclear tests. Megalon arrives at the empty lake bed and proceeds to destroy poor Tokyo, guided by Jet Jaguar. Meanwhile, Goro and Roku, tied up inside a truck trailer, work loose the ropes binding them and try to figure out a way to escape. Jinkawa overpowers his Seatopian captor and rushes off to find his friends.
Grabbing the other Seatopian and throwing him off the truck, the drivers were trying to dump the truck's cargo (Goro and Roku) into the dam! Megalon shows up, scaring the drivers away. Jinkawa tries to get the truck bed down so he can free his friends, but it slips and Megalon hits it like a tennis ball. Once free, Goro takes off in a helicopter to find his rebellious creation.
Using the override control, Goro instructs Jet Jaguar to go and get Godzilla. Godzilla, upon hearing what Jaguar has to say, is outraged. He jumps into the water and heads for Japan. Jet flies back to Japan and does a neat trick:

He increases his own size to about 500 times what he was before and starts pounding the hell out of Megalon. Upon seeing this, the Seatopians ask Space Hunter Nebula; Universe M for help. The Nebulans send Gigan, their cyborg. Gigan comes and knocks Jaguar senseless. The two gang up on Jaguar and just about finish him off before Godzilla arrives. Finally, a tag team battle ensues. By the end of the movie, Godzilla drives off Gigan, then he and Jaguar gang up on Megalon. An embarrassed, defeated Megalon goes back to Seatopia. Godzilla returns to his island home, and Jaguar returns to his original size.

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