After the battle against Zogu was over, both Gamu and Fujimiya began to live normal lives until another threat arrives on Earth - a surviving monster soldier of Zogu's army named Gakuzom.
In 1933 New York, an overly ambitious movie producer coerces his cast and hired ship crew to travel to mysterious Skull Island, where they encounter Kong, a giant ape who is immediately smitten with the leading lady.
Zero finds himself trapped within a universal gap and faced against an impostor Ace. Following the battle, Darklops Zero was restrained once more by Herodia, remembering a figure named "Kaiser Belial" before deactivating. Rei was restrained after his failed attempt to intrude the alien base but was rescued by none other than his alternate self. Unlike the prime Rei, alternate Reimon was never able to control his powers, forced into the state of Reionic Burst until the original Rei punched Reimon, thus deactivating its Reionic Burst mode. Rei revealed that he lost his Rayblood instinct after Hyuga threw Seven's Eye Slugger, creating a scar on his chest which symbolizes the former's friendship with ZAP SPACY members. While searching for Rei, Hyuga instead finds his Neo Battle Nizer and an entrance to the alien base made by Litra. Although the fake Ace was destroyed, Zero try to find an escaped but was halted by Seven and Ultraman impostors.
Japan is thrown into a panic after several ships are sunk near Odo Island. An expedition to the island led by Dr. Kyohei Yamane soon discover something far more devastating than imagined in the form of a 50 meter tall monster whom the natives call Gojira. Now the monster begins a rampage that threatens to destroy not only Japan, but the rest of the world as well.
Two fishing scout pilots make a horrifying discovery when they encounter a second Godzilla alongside a new monster named Anguirus. Without the weapon that killed the original, authorities attempt to lure Godzilla away from the mainland. But Anguirus soon arrives and the two monsters make their way towards Osaka as Japan braces for tragedy.
At the turn of the century, all of the Earth's monsters have been rounded up and kept safely on Monsterland. Chaos erupts when a race of she-aliens known as the Kilaaks unleash the monsters across the world.
Searching for his brother, Ryota stows away on a boat belonging to a criminal alongside two other teenagers. The group shipwrecks on Letchi island and discover the Infant Island natives have been enslaved by a terrorist organization controlling a crustacean monster. Finding a sleeping Godzilla, they decide to awaken him to defeat the terrorists and liberate the natives.
Gaira, a humanoid sea beast spawned from the discarded cells of Frankenstein's monster, attacks the shores of Tokyo. While the Japanese military prepares to take action, Gaira's Gargantua brother, Sanda, descends from the mountains to defend his kin. A battle between good and evil ensues, leaving brothers divided and a city in ruins.
During WWII, Germans obtain the immortal heart of Frankenstein's monster and transport it to Japan to prevent it being seized by the Allies. Kept in a Hiroshima laboratory, it is seeming lost when the United States destroys the city with the atomic bomb. Years later a wild boy is discovered wandering the streets of the city alone, born of the immortal heart.
The advertising director of Pacific Pharmaceuticals, frustrated with the low ratings of their sponsored TV program, seeks a more sensationalist approach. He orders his staff to Faro Island to capture King Kong for exploitation. As Godzilla re-emerges, a media frenzy generates with Pacific looking to capitalize off of the ultimate battle.