At the R&D Headquarters in San Diego, California, Steven Woods is being interrogated by a military officer, who assures that Allison will be fine, but asks about the aliens Allison saw. Woods tells the officer that Allison saw a man come in, change forms and kill everyone in the facility. The officer questions this, asking for what purpose would an alien race take a Godzilla specimen, plus why something would attack the USS Goldenstein. Woods says that he doesn't know the answer to either question, and that he was not aware the ship had been destroyed. The officer explains that it was destroyed by what could have been a squid or a snake, and that the reactor is missing. When Woods asks for Godzilla's status, the officer replies that they've deployed some ground units which will be approaching Godzilla via the sea. Woods then tells his men to suit up, as Godzilla's going to have some company.
Many live news reports start being broadcasted as Godzilla lies on the ground, seemingly dead. However, multiple Aggregate Destoroyahs come and latch onto Godzilla, waking him up. Godzilla stands up and unleashes a nuclear pulse which kills the Destoroyahs. While Godzilla stands still in the beach, Lucy and her fellow megazoologists-in-the-making are at the Beijing Capital International Airport. Kristina Sumres asks what the things attaching themselves to Godzilla are, to which Lucy explains they are crustaceans, and concludes that all these new creatures (Gezora, Manda, and the Destoroyahs) must be appearing for a reason. Dr. Ando asks why would they be appearing, and Lucy replies that she doesn't know, but she tells herself that Godzilla could be the reason.
Back on the shorelines, a giant, flightless Destoroyah surfaces and starts to battle Godzilla. Godzilla and Destoroyah exchange beams, but Destoroyah is not damaged and slams Godzilla on the ground. Godzilla hits Dez with his tail, only to have Destoroyah grab Godzilla with his tail and slam him on the floor once again. The military arrives and starts attacking Destoroyah, but Destoroyah's wings unfold as he takes to the skies and destroys all the craft. The Cryogs are monitoring the fight and claim that Destoroyah's power might make it so phase two of their plan wouldn't be necessary. The Cryog leader congratulates the Devonian commander on Destoroyah, and the Cryog reminds the Devonian that this plan must work and that the Cryogs cannot stay in space forever. The Devonian says that they are analyzing the Godzilla DNA and have found an island to test a possible terraforming of on. The leader again congratulates the commander, when he is interrupted by Mothra heading towards the battle of Godzilla and Destoroyah.
Destoroyah is thrown over by what is revealed to be Mothra. Destoroyah shoots his Micro-oxygen Beam at Mothra, which she dodges, and then uses his tail to catch her with. Just then, Godzilla surfaces from the ocean with the USS Goldenstein's missing reactor. Destoroyah throws Mothra to the ground and is headbutted by Godzilla in the chest, followed by a blast from Godzilla's Atomic Breath. Destoroyah is still not affected by it and fires his micro-oxygen beam at Godzilla, when Mothra dives in and hits Destoroyah, followed by him having his tail grabbed and then being slammed on the ground by Godzilla. Right then, two twin Mothra larvae come swimming from the ocean as broadcasting of the battle is cut, and Dr. Ando says they'll have to go in jeeps.
Back in the battle site, Mothra releases her scales upon Destoroyah, which Destoroyah retaliates to by using his Horn Katana on her. Mothra hits the ground, and Godzilla grabs Destoroyah's horn and rips it off. Godzilla starts using his Atomic Breath against Destoroyah and the larvae use their web to trap Destoroyah. The web completely cover Destoroyah, and the Aggregate forms start emerging from the cocoon. Godzilla incinerates them all, and says farewell to Mothra and her larvae, who gently put her wings on their backs and ferry her across the sea. Woods and his soldiers arrive when the battle ends, and he points out that Godzilla took the Goldenstein's reactor to lure Destoroyah to shore and have better chances against the crustacean in a battle with Mothra.
Meanwhile, Lucy and the others have arrived at the site where an unknown kaiju have been spotted, whom the government has asked them to help find. Just moments later, Lucy tells anyone who is still able to take pictures, as most of their batteries have died, to do so of something unbelievable rising from the waters, Varan. However, the soldiers insist this monster is not the one being looked for.