"San Diego has become the latest victim of a monstrous invasion from the sea. With Godzilla recovering from his last destructive battle it's up to a familiar face to fight off the mysterious Destoroyah swarm!"
SPOILER WARNING: This section may contain major plot and/or ending details. Proceed at your own discretion.
In San Diego, California, at the Science Division of the CKR Headquarters, Steven Woods is greeted by a Mr. Allison after he and his crew arrived there. Woods says they brought pizza, the mysterious leg that fell off of Zilla in Hawaii, and a chunk of Godzilla's skin. Allison asks what's wrong with Chavez as he sees him coming off the plane with a bag, and Woods replies that he hates flying, but doesn't mind sitting next to a piece of radioactive Godzilla hide. Meanwhile, the CKR Headquarters is being monitored by the alien race that appeared briefly in the first issue, and one of the aliens disguises itself as a human to go after the Godzilla skin after noticing that it is being taken inside. Allison and Woods continue talking, first about a new weapon made from the absolute zero cannon from the last MechaGodzilla, called the "Ice Box." Allison states that a direct shot will do some damage if the kaiju are hit in the eyes, but the main theory is to pick at them bit-by-bit. Woods replies that the eyes thing doesn't work. Allison says that the weapon can be used to freeze small ports of a monster, as the ice explodes, the weapon could be useful, and that he has a few ready for Woods' team. Woods asks if the government has moved on to these types of weapons and is done with giant robots, to which Allison replies no, and that new members from the Monster Kill Crew that have experience building them have been added to the ranks after being given a choice of either hard time or hard work because of threats they had made against the world's governments.
A Cryog, in a human disguise, walks towards the entrance to the headquarters. A guard stops it, and the Cryog asks about a transport plane that arrived there a short time ago. The guard refuses to answer, and the Cryog grabs him by his neck with its tentacle, and asks where it was delivered. The guard tries using his gun, but the Cryog doesn't allow it. The guard points to a warehouse nearby, and the Cryog says "thank you" before snapping the guard's neck. The Cryog then tells the alien strike team to commence landing.
Miles from the CKR facility, several Aggregate Destoroyahs surface from the ocean and invade Ultra Convention VII. At first, the people confuse the Destoroyahs for detailed suits but realize they're real when the Destoroyahs attack. Bullets prove ineffective, and the San Diego police department calls for help. 200 miles away from the California coast, the USS Goldstein is out at the ocean protecting the people living at the coast. However, Manda attacks the ship and the aircraft carrier explodes, with what's left of the crew being attacked by Gezora. Back in San Diego, Woods and his team arrive and start fighting the Destoroyahs. They try using their machine guns, but they barely scratch the creatures. Woods asks HQ if there are any other weapons, but no one responds. It turns out the Cryogs have secured Godzilla's skin, and they bring it aboard their spacecraft. The aliens seem to want the Earth as a home for themselves, and assure that the humans will be wiped from the planet in due time. Woods tries to get the ice boxes working as everyone runs out of ammunition. Just then, a girl is cornered by a Destoroyah as it sticks out its toothed tongue to eat her. Woods tackles it and completely uses up the magazine of the machine gun, but Destoroyah uses its tongue to cut a piece of Woods armor down to his skin, making him bleed. Woods uses a knife on the Destoroyah and grabs the girl, and just as the Destoroyah was to attack them, it appears frozen. A member of Woods' team got the ice box to work, and so they use them on the Destoroyahs. Woods tells Chavez that they'll need to get a containment team down there to gather all they can of the Destoroyahs, which seem to dissolve when frozen. Both say they can't communicate with HQ, and Chavez states that the Destoroyahs look like the crab leg found on Zilla. However, the one on Zilla was much bigger than the ones these Destoroyahs have, and that perhaps the Destoroyahs they fought are babies.
Godzilla surfaces nearby the wreck of the USS Goldstein, but is pulled underwater by an unknown creature, and Woods and his team head back to the CKR Headquarters. They find Allison is the only one remaining, but he starts shooting at them, paranoid. Woods orders his team to hold fire, and hides behind a car. He orders Chavez to pull his trigger before Allison if Allison shoots. Woods takes off his helmet and walks towards Allison unarmed. Allison warns Woods to stay back, and demands to know if Woods is really human, as Woods states that they both know that he's a lousy shot. Allison tells Woods he doesn't know what he saw and then faints. Meanwhile, on the Cryog ship, the leader states that everything is going as planned, but asks if the Godzilla skin is enough to work with. The Cryog that was on the CKR HQ said that it was sufficient, but all of it would have to be used, and that if the new creature did as it should, Godzilla would end up being nothing more than carrion. The Cryog then asks how would they free the captive monster from its stasis, to which the leader replies that they just need to create another one in a populated human city, and they are ready for that. Back in Malibu, California, Godzilla appears with a scar on his chest, and he collapses to the ground.