The film opens with a monologue of atomic bombing tests were done in Japan back in 1945. 9 years later in the year 1954, a giant reptilian creature called "Godzilla" appears, having been awoken and mutated from the bomb tests and he rampage through Tokyo, killing and destroying anything in his way. However, one scientist named Dr. Serizawa creates a Weapon known as the "Oxygen Destroyer" and with it, he successfully kills Godzilla (sacrificing himself in the process,) thus ending the Monster's attack on Japan.
Parts 1 and 2
61 years later in the present, an alien named Dogolas finally discovers Planet Earth in his search to find a new home, and he plans on terraforming the Earth for his own benefit by starting an invasion of the Planet. To begin his conquest, Dogolas sends two unknown mutations (which he plan have continually get stronger once they fully mature) as well as the monster King Ghidorah to attack the Earth's more populated regions, starting with Japan. King Ghidorah proceeds to fly to Japan and begins attacking Osaka. Suddenly during the Space Monster's rampage, Godzilla appears! Dogolas identifies that this Godzilla is a second, more powerful one than the original. Believing that Godzilla would be a threat to his plans, he has King Ghidorah battle with the new Godzilla instead. Godzilla and King Ghidorah proceed to face off in a vicious battle until finally, Godzilla defeats King Ghidorah by severing his center head with his Atomic Ray. Enraged that his Monster has been defeated, Dogolas recalls King Ghidorah's body back to his ship, while Godzilla heads further inland to an unknown territory. Meanwhile on Infant Island, a Larva Mothra hatches and swims away to an unknown location as well.
Parts 3 and 4
Having left the City, Godzilla has now wandered to an open-field, when the beast encounters Mothra during his journey. Godzilla initially ignores her, but he quickly becomes provoked when she smashed a boulder against his head, causing him to attack her. Despite some impressive maneuverability from the Larva Mothra, it's ultimately not enough to stop the bigger, stronger Godzilla, who defeats her after a short battle, trapping under a giant tree. As he leaves though, Godzilla soon remembers that the Mothra he just fought was the offspring of its Mother, Mothra Lea, who once helped his father in battle against a Titanosaurus, which fills the monster with shame for his actions.
Suddenly during Godzilla's lament, he is confronted by Dogolas's next Monster: another Godzilla! The two godzillas battle fiercely until the main Godzilla fires his atomic ray at the doppelganger, exposing a mechanical body underneath it. Soon enough, Dogolas burns his monster's remaining skin away to reveal that the beast was actually Mechagodzilla! Dogolas orders the mechanical saurian to destroy Godzilla, and the robot attacks Godzilla once again. However just when it seems Mechagodzilla is about to gain the upper hand, Mothra appears (having managed to free herself from the tree she was trapped under, and after witnessing Godzilla's battle,) she saves Godzilla from one of the Robot's attacks. Eventually, with Mothra's assistance, Godzilla manages to destroy Mechagodzilla by blasting his chest. Dogolas, frustrated from Mechagodzilla's defeat, now sends yet another unknown beast to attack Godzilla.
After Godzilla and Mothra defeated MechaGodzilla, Godzilla realized that Mothra was the one who saved him and aided him. Suddently, the two Kaiju hear a loud echoed cry from a nearby swap. Godzilla first attempts to destroy the swamp with his atomic ray, but is stopped by Mothra. Then, the two headed over to the swamp, but when arrived they were soon surrounded by a fog. Abruptly, a large predatory plant-like vine emerges from the fog and has captured Mothra. Meanwhile, Godzilla keeps heading fowards, unaware of Mothra being taken, and stumbles upon another vine that emits the cry he has heard before. Curious, Godzilla follows the vine only to realize that several others like him have kidnapped Mothra and that they are actually part of none other than Biollante! The massive reptile plant emerges from beneth the swamp and orders her vines to further injure Mothra. Much for Godzilla's frustration, the dinosaur started wading towards Biollante, and in respond the plant monster sends her vines and even builds a wall made from plants, but all are quickly destroyed by Godzilla's atomic ray. Biollante decides to use a different strategy: she dodges Godzilla's ray and emeges again from behind him. The creature fires her green sap at Godzilla, weakening him enough to be able to bite him on the head and slam him against a large rock. Mothra notices Biollante's attacks and fires her energy blasts at her. The beast roars in pain and starts sending more vines as Mothra's blasts become stronger. Eventually, Mothra's blasts hit Biollante's core several times which provokes her and causes her to fire her sap at her and one of her larger vines. But just as the vine is about to hit Mothra, Godzilla returns and takes the hit, creating a large hole in the right side of his chest. However, Godzilla ignores the pain and regenerates his wound. Godzilla then rampages towards Biollante and finishes her off with his spiral atomic ray, setting a large fire in the swamp and causing the plant monster to explode. After seen his monster fail, Dogolas becomes angry and realizes that Godzilla is a threat to his invasion and he has to be destroyed.
After defeating Biollante, Godzilla takes the injured Mothra to a secluded countryside, where she begins her metamorphosis, sealing herself inside of a cocoon. With Mothra transforming, Godzilla is left to watch over her while she is in a more vulnerable state, guarding it from any monster that might attack it. While doing so, Godzilla remembers another memory of his past, one in which that involves himself, his father, and Mothra Lea. When he was younger, Godzilla recounts a friendly encounter he had with Mothra's mother as well, while leads him to tearfully remember his first fight with Mothra once more, this time in a more regretful manner. While lamenting however, Godzilla is attacked by a stray Gyaos, who has ambushed him in an attempt to eat Mothra's Cocoon. Godzilla and the Gyaos to battle, but ultimately the Monster King triumphs, blowing Gyaos to pieces with his Atomic Ray. After which, Godzilla proceeds to eat Gyaos's remains, only to fall asleep shortly after.
Meanwhile on Dogolas's ship, the alien analyzes King Ghidorah's body, noting that its middle head was severed. During his research, he discovers some of Godzilla cells present in Ghidorah's body. Realizing what he can do with the cells, Dogolas plans to fuse Godzilla's and King Ghidorah's cells into a creature of Myth named "Bagan," hoping to boost its power exponentially and use them in his plans for conquer of earth. Time passes and night falls, during Godzilla's slumber, Mothra completes her metamorphosis and she soon emerges from her cocoon in her Imago Form. Upon noticing Godzilla sleeping, Mothra is prepared to wake him up, only to discover a nearby hissing noise as well... Which is soon revealed to be Dogolas's 2nd Monster Mutation: Megaguirus.
- Godzilla (ShodaiGoji, TokyoGoji, MogeGoji, ShodaiSupaGoji)(BioGoji in part 6)
- Mothra (TokyoMosuImago, TokyoMosuLarvae)(later HeiseiMosuLarvae & HeiseiMosuImago)
- King Ghidorah (HeiseiGhido) (Part 1 & 2 as Wii and Part 6 as PS3/PS4)
- Titanosaurus (ShodaiChitano)
- Fake Godzilla/Kiryu (ShodaiGoji, MireMekaGoji)
- Biollante (ShodaiBio)
- Mecha-King Ghidorah
- Originally, a humanoid version of Monster X was supposed to be the alien to have invaded earth and control the mutants. However due to a suggestion by cast member Goji73, he was replaced by Dogolas as he bore a resemblance to the unnamed Aliens of the original game.
- Additionally, Alien Baltan (from Ultraman) was supposed to be the mastermind behind Dogolas but he was scrapped for unknown reasons.
- Unlike the Video Game in which it is based on, the Mechagodzilla incarnation in this fanfilm will be that of Kiryu.
- Despite not appearing in the Video Game, Titanosaurus makes an appearance in Part 3, as an antagonist who battled Godzilla's father in the past. Titanosaurus was confirmed to return for Part 6 along with Gabara, another monster who was not included in the video game.
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