In beautiful San Francisco, something has gone awry in an earth-shattering way. Entire buildings, even whole city blocks, are being swallowed up into the earth, only to fall and smash to pieces on a vast cavern floor deep below. Unbeknownst to all, great orange-and-gray quadruped equipped with a giant gear on the end of its tail, goofy antennas on its head, and a mouth like a steam shovel is lurking underground, digging tunnels and eating up the demolished buildings that fall through.

Back on the Calico, Brock (the token black character with an afro) and Pete (the Kenny) go looking for Godzooky, whom just happens to be underneath the boat. Apparently at some point he learned to swim—an ability he hadn't developed in the last episode. Quinn, the female member of the crew, is going to a science conference in San Francisco. However, when they approach the city, it is obvious that something is wrong. On the Golden Gate Bridge everyone in the city is trying to leave—and, even though only the outgoing lanes are filled with cars, the bridge can't take the weight and will collapse at any moment!

There's only one thing to do—Captain Majors uses his giant, remote control Godzilla! The Big G bursts out of the water with a roar and solves the problem by tearing off a huge chunk of the bridge and carrying it and the cars still on it over to a hill and placing it down there. The crewmembers of the Calico cheer on Godzilla as he sinks back underwater. His work here is done.

Captain Majors, Quinn, Brock, Pete and Godzooky go for a drive around San Francisco, which they find to be quite a mess at this point. Gigantic holes that appear to have been made by some immense creature are ubiquitous. The adults, being intelligent and rational folks, tell Pete and Godzooky to wait outside while they climb down the hole on foot without any weapons of any sort. Suddenly they hear a loud pounding/crunching sound that seems to be coming closer, and the whole street underneath the jeep (on which Pete was waiting) opens up. The jeep, along with Pete and Godzooky, are sucked underground, but the imperiled pair are miraculously unhurt. Pete finds a tunnel in the hole, and the entire crew of the Calico decide to explore it together in the jeep—despite the fact that they still have no weapons, they can't drive out because of the hole, and the ground has a tendency to shake which would seem to indicate that the tunnels could collapse at any moment.

After driving for some time, they come across a cavern—and the dreaded and dreadful Eartheater! Captain Majors puts the pedal to the metal, trying to drive back the way they came—but the Eartheater shoots sonic rays from its goofy antennas to block the tunnel and keep them from escaping. Captain Majors then has a brainwave—the monster lives underground, so it is probably sensitive to light! He turns on the jeep's headlights, and his hypothesis proves correct; the light drives the Eartheater away. Our heroes find an alternate tunnel back to the surface.

Unfortunately, the Eartheater follows them. The Eartheater seems to have forgotten that it was sensitive to light and seems pretty comfortable with daylight as it emerges. Carl tries to call Godzilla, but he has lost the remote beeper device! Pete improvises, telling Godzooky to call Godzilla, and the green thing promptly makes really obnoxious noises which prove just as effective as the Carl's buzzer system in summoning the Big G. The King of the Monsters bursts out of the water and starts heading their way.

The humans are still in a lot of trouble, however. The Eartheater will soon be upon them. Captain Majors jams on the accelerator, but the jeep is stuck in some mud. Godzooky rushes to help by pushing the car, and strangely has a rather hard time of it—especially since he was shown carrying the vehicle moments before. Nevertheless, just in the nick of time, Godzooky manages to dislodge the jeep, which then speeds down the road. The Eartheater chases them, only to run into Godzilla.

The two monsters roar at each other a lot until Godzilla blasts the Eartheater with his laser beam eyes. The Eartheater returns the favor, blasting Godzilla backwards with his sound waves before making his escape by zapping open a tunnel with his antennas.

Our heroes go back to the Calico to plan their attack. This time they will use gas canisters that have tranquilizing properties. They drop the canisters down all the giant holes in the city, thus blocking the creature's escape and trapping it underground where the smoke should put it to sleep. Unfortunately, someone forgot that the beast can burrow, which it does—bursting up right between our heroes and their jeep. Godzooky once again calls Godzilla for help, and Captain Majors, Quinn, Brock, Pete, and Godzooky all jump on a cable car to escape, with the Eartheater close behind. It uses its sonic waves to blast at Godzooky, narrowly missing. Suddenly our heroes find themselves with a new threat—their combined weight has made the cable car uncontrollable! Once again, Godzilla has to bail their fannies out of the fire.

After the rescue, Godzilla takes on the Eartheater in a rematch, sending a stream of nuclear breath towards it and narrowly missing. They trade more explosive rays, then engage in some titanic wrestling before the Eartheater breaks away and disappears somewhere in the concrete jungle.

Godzilla, quite frustrated, stomps about through the city, searching for the dirt-muncher. Turns out the monster that has lived its entire life underground has chosen to hide by climbing high on the remains of the Golden Gate Bridge. Godzilla, still quite peeved, zaps at him with his laser eyes while the Eartheater zings Godzilla with his sonic beams. Godzooky tries to help by flying around in circles. Finally, through their combined efforts, the bridge collapses and the Eartheater falls in the water, where he disintegrates into a pile of mud. Godzilla walks over to the mud pile and makes a noise that sounds a lot like "yeah."

Their mission completed, our heroes leave the scene on the Calico—but something is mysteriously slowing them down. Is it the mud? No, Godzooky is waterskiing!