Out on the ocean, Pete is trying to get Godzooky to play fetch with a stick—but Godzooky comes back with a boat instead. Meanwhile, Brock realizes they are passing over Atlantis. Quinn insists that Atlantis is not real, Carl insists it is real. Suddenly their sensors pick up a strong quake. Underwater, unbeknownst to them, a city is rising from the ocean floor!

On the sensors Brock sees that something big is heading for the Calico! They kick the Calico into full speed ahead, and get out of the way just before the city comes out of the water. Our heroic heroes come in for a closer look, but then one of the futuristic buildings shoots the Calico with a ray of light which cuts off the ship's power while drawing the boat towards the mysterious city via some sort of tractor beam. Thus clever Carl calls Godzilla to save his keister. Godzilla uses his mighty muscles to hold the boat back, but the power of the city is so enormous that Godzilla has a tough time of it. (Miraculously the Calico doesn't just smash apart.) As Godzilla is fighting on with all his strength, a second mysterious ray transfixes the gargantuan green one and makes him disappear! With Godzilla gone, the boat is brought in to the city with no further trouble, but Godzooky is left outside.

The Calico is held inside a tunnel in the city, and the walls close in from the sides. Godzooky busts a hole in the ceiling of the tunnel and saves our homo sapiens heroes moments before the walls crush the Calico into calicrud. Outside in the fantastic cityscape, Pete, Carl, and Godzooky take off searching one way, Brock and Quinn another way—all of them looking for the vanished Godzilla.

Meanwhile, the blinking lights on one of the buildings trigger a mechanism that releases a ridiculous menacing robot that has no arms or legs.

Quinn and Brock wander into a special view-screen equipped building and watch some history discs that reveal how Atlantis was sunk by an earthquake, but everyone was put into suspended animation before it could destroy them. While all this was going on, some dude named Kara-El (not to be confused with Kal-El) attempted to convince them that the best strategy was to use a time machine to solve their problems instead, but failed and was stuffed into suspended animation as well.

While Quinn and Brock stuff knowledge in their brains, Pete and company find the multitudes of sleeping people, and the evil robot attacks our heroes with death rays and protrudes robo arms from its sides. In the chaos, the robot accidentally blows up a building, revealing Godzilla in suspended animation.

The robot has another kind of ray which melts stuff, which it uses to liquefy the obstructions that Pete and crew were hiding behind. Meanwhile, Quinn and Brock, ever the inquisitive minds, go back in time using the time machine, back to when Atlantis is about to die. Thusly Quinn and Brock are forced into the suspended animation circles along with the all the rest of the Atlanteans.

Back in present time, Pete and company are being chased by the malevolent machine of evil and hide in a building. Our heroes find Quinn and Brock in suspended animation, but then a voice from a mental projection of Kara-El tells them their friends are safe, but that he can't help them because the "Colossus" (that being the malicious mecha outside) suffered a malfunction in the Atlantis-dooming quake and became an evil creature which has kept everyone in suspended animation for all eternity. The only way to wake the Atlanteans (and the rest of the crew of the Calico) is to destroy the robot!

In an attempt to defeat the computerized cretin, our heroes try to get the Colossus to free Godzilla. Godzooky flies around in the sky, trying to coax the Colossus to shoot at him and wake Godzilla instead. It works. Godzilla revives and blasts the Colossus with his trademark flame attack, but the massive machine comes on undaunted. Godzooky sprays some smoke, and completely fails to help. The Colossus zooms at Godzilla, but our favorite radioactive reptile jinks away and the robo levels another building instead. In an effective counterstrike, Godzilla relieves the relentless robotic renegade of one of its arms by zapping it off with his energy eye-beams. Pushing his advantage, Godzilla grabs onto the robot with his claws, but then the callous Colossus grows super crazy tall with Godzilla still holding on, then spins wildly until Godzilla is thrown off into a nearby building. The big bad 'bot then proceeds to grab Godzooky in one of its pinchers, and Godzilla, incensed, yanks off the offending pincher with a spectacular jerk. Oh, but no! The robot has a ton of other arms which extrude from somewhere inside with which it grasps Godzilla! But no matter how many arms the robotic rebel may have, Godzilla still kicks more butt. Our scaly champion chucks the computerized creep into the water, which short circuits the Colossus and causes it to break apart. All the Atlanteans, along with Quinn and Brock, are awoken, and there is much to celebrate.

Kara-El is very thankful and sends our heroes via the time machine back to their boat before it was crunched into matchstick fodder. (Somehow this doesn't bring the evil robot back to life.) Then, as our protagonists gawk, the whole city of Atlantis turns into a spaceship and flies away—they were all aliens the whole time!