The famous Taylor's comet streaks through space above earth. Below, the Calico is in a big and nasty storm, caused by the comet's celestial passing. After a time of being battered around by crazy strong winds, the ship crashes into a reef, puncturing a hole in the Calico's side. Water sprays through the hole, dousing a sleeping Godzooky, who plugs the leak with his hand.

A reef might suggest that land is nearby, but the crew can spot nothing of the sort. Then, suddenly, they see their own ship charging at them across the ocean waves! But, no! It was a reflection in a force field that just happens to be out in the middle of the ocean! Some lightning strikes and breaks the force field, and then our heroes find an island hidden behind it.

Meanwhile below deck, Godzooky can't keep the water back for long and the ship is flooded. Godzooky calls Godzilla, who does his usual roaring routine before picking up the boat and carrying it to land. Godzooky flies up to Godzilla, happy to see him, and Godzilla blasts the winged lizard away with his breath, triggering more hijinks with Godzooky and a palm tree. Godzilla, sensing a job well done, departs, and our heroes decide to go to sleep while the storm persists.

Unfortunately, outside, there is a terrible monster looking down from a nearby mountain!

The force field has come back on after the storm ends, and the protagonists are trapped on the mysterious island. Quinn, Pete, and Godzooky go out on a mission to uncover the source of the force field and devise a way to escape. Soon enough they discover a crystalline machine sticking out of the ground. Godzooky also finds a giant hoof print, and suddenly the monolithic monster from before appears from nowhere—a big-mouthed Cyclops with huge claws and hooves! Naturally it cuts everyone off from returning to the Calico and tries to stomp on Godzooky.

Carl and Brock see the trouble and call Godzilla for help. But Godzilla is blocked by the force field! Apparently he can't break through, even though lightning did the trick earlier!

Quinn and Pete hide in a crevice, but Carl and Brock are menaced now, and Godzooky saves them. Unfortunately for Zooky, the Cyclops monster grabs him in its claw.

Sensing Godzooky is in trouble, Godzilla becomes completely enraged. The Cyclops takes Godzooky into a canyon that the humans impossibly know leads to a dead-end. Carl and the others follow the gigantic Cyclops inside, and there they see Godzooky apparently free and flying around, but in actuality it is just that the one-eyed fiend is invisible and holding bat-lizard up in the air. The mono-irised monstrosity begins to build a wall of rocks to trap the humans inside, so Quinn leads everyone into a cave, which has the history of the island written on the walls in cave paintings. The story goes that a number of outer-space aliens that look suspiciously like Ultraman landed on the island many years previous and were attacked by the murderous and super-big Cyclops. The Harryhausen-inspired freak was too much for them, and the aliens created the force field to protect the earth from the monster. Godzooky finds another way out of the cave. The humans run to the crystal machine they found earlier in hopes of weakening the force field enough for Godzilla to enter—but the Cyclops is close behind! Quinn (a real super genius) figures out how to operate the machine and Godzilla comes stomping onto the island. The two monsters pose dramatically at each other for a while, giving the humans time to escape.

Quinn needs to solve the problem of the monster, and comes to the utterly brilliant conclusion that they need to turn on the force field without getting trapped on the island.

In the mean time, Godzilla and the Cyclops fight a lot. The Cyclops can shoot powerful bursts of energy from its eye, so they both have a zapping good time. Our heroes take the opportunity fix the boat, and Quinn constructs a timer device that should be able to activate the force field after they leave.

Godzooky tries to help the Big G fight, but only manages to get in the way, so Godzilla scolds him. The depth-perception impaired beast and Godzilla continue to fight, and the Cyclops becomes invisible. Quinn sets the timer for five minutes, and the Cyclops monster chooses this time to retreat.

Godzilla and the humans flee from the island. But as they are running, the Cyclopian adversary appears in the water and attacks Godzilla, this time utilizing his invisibility powers to give himself an unfair advantage over our favorite irradiated Japanese mutant.

Brock and Pete fly up in the copter, aiming to equalize the odds, and throw lots of paint that they apparently keep in stock on the Calico for situations such as this. Godzilla lifts the paint-splattered punk Cyclops and lobs him towards the island, then turns on his heel and sprints for open water with the Cyclops in hot-headed pursuit. But just then the force field comes back on, trapping the single-eyed titan inside.

As the Calico floats away, Godzooky plays with a shell that he found on the island. Pete tells him that if he puts the shell to his ear, he can hear the ocean. Godzooky tries it, and dumps the water inside all over his head.