One day in Chicago Illinois, a couple is seen proposing to one another. Their proposal however is cut off by an enourmous unseen figure as they scream in terror. Shortly after, Chicago is attacked by many giant monsters, including Godzilla, Anguirus, Manda, Gezora, Ebirah, Varan, and Zilla, who all cause massive destruction all throughout Chicago. At the same time, a man named Lieutenant Matt Kennedy (nicknamed Razor Shark) is called in by Commander Amanda Lexington, who informs him on the situation in Chicago, as well as Godzilla's history and his last appearance since "Operation: Destroy all Monsters" back in 1999. She then informs Matt that he will be piloting the "X-Rider," a top-secret military weapon that will help the military in fending off the invading monsters.
After going over the X-Rider's functions, as well as it's prime ability to reflect Godzilla's Atomic Ray via a "Fire Mirror," Matt and the Military are sent into action against the rampaging monsters. Despite their efforts though, they are only able to evacuate civilians while fending off Manda and Zilla at the same time, and sure enough their efforts are in vain against the combined might of Godzilla, Anguirus, and Varan. It is then revealed by Captain Kumi Wakabayashi that the appearances of the monsters was not by their own will, but rather due to a mysterious EMP having released and "teleporting" them off of Monster Island, but by whom remains a mystery. Capt. Wakabayashi then informs Commader Lexington's team that the GDF has already prepared to fight back against the monsters with Mechagodzilla, having taken the remains of the original robot and modifying it into their own weapon. Mechagodzilla is then launched in Japan and heads off to Chicago.
Meanwhile back in Chicago as Matt is preparing to fight in the X-Rider, he is confronted by the Shobijin, who inform him that despite the actions of the monsters, they are not his enemies, and that "a great force" has taken control of them in order to destroy the city. Despite Matt's doubts and brash response, the Shobijin also inform them that Mothra and Gfantis are on their way to hold off the monsters until whatever is controlling them is found and stopped. Once Matt and the X-Rider are launched into action, the weapons of the X-Rider prove valuable as it and the combined might of the military are successful in killing Ebirah and Gezora. However despite putting up a decent fight against Godzilla, it is forced to temporarily retreat after taking some damage from Godzilla. Fortunately, Mechagodzilla, Mothra, and Gfantis all arrive to do battle with the remaining monsters, with Mechagodzilla battling Varan, and Mothra and Gfantis battling Godzilla and Anguirus respectively.
At that moment, Matt, the Military, and the GDF notice via infered vision that the monsters' actions are being controlled by an invisible UFO. When contacting the UFO, its carrier reveals the true mastermind behind the monster attacks: An Alien known as "Queen Xaxious" whom has enslaved the monsters in her plan to conquer the Earth. While Queen Xaxious gloats in her supposed victory, her satellite dish that is controlling the monsters is destroyed by Matt, freeing all of the monsters from her control. Despite the setback though, Queen Xaxious has Plan B in effect by releasing more monsters (of alien nature) to fight for her, the likes of which include Gigan, Hedorah, and "Zombie Kong." Additionally, Ebirah is revived by Queen Xaxious's lackey, Sargyle, and Mechagodzilla is overtaken by Sargyle as well, who hacks his system and causes Mechagodzilla to go berserk against the Earth Monsters. Lastly to ensure that the Earth Monsters don't recieve any help, she shoots down Matt and the X-Rider.
As Queen Xaxious's monsters engage the Earth Monsters in battle, Matt is left to repair what he can of the X-Rider. During his repairs though, Hedorah is blasted by Gfantis and inadvertantly releases spawns of toxic creatures known as "Slugs" (by Queen Xaxious) who attack Matt and the Military below. While the Military manages to hold off the Slugs relatively fine, Matt has some difficulties as one ambushes him. With the help of the Shobijin, Matt manages to kill the last of the ones attacking him and resumes repairing the X-Rider, while the Shobijin revive Mothra (whom had earlier been incapacitated by Godzilla.) Realizing that her monsters are starting to lose, Queen Xaxious orders Sargyle to release even more of their monsters to fight, which now include Rhiahn, Orga, and even Zigra. With all of the Space Monsters released, Godzilla and the Earth Monsters charge into battle, and an all-out Battle Royale commence between all of the monsters.
In the ensuing battle, Godzilla and Zombie Kong engage in battle. Despite some powerful attacks by Kong, Godzilla manages to power through and blasts Zombie Kong with his Spiral Ray, seemingly killing him. In doing so however, Godzilla also has depleted all of his energy. With the opporitunity, Queen Xaxious and Sargyle have all of their monsters focus their attacks on the weakened Godzilla, in the hopes of killing him the soonest. Lastly to assist them, Queen Xaxious unleashes her final monster, Biollante. Sure enough, Godzilla is no match for the onslaught of attacks by the Space Monsters and Biollante, and ultimately he is beaten to near death by them all.
Before Godzilla can be finished off however, he is rescued by the timely appearance of Mothra, who instills some of her energy into him. At the same time, thanks to the intervention of the Military, Mechagodzilla's programming is overridden from Sargyle's control and Mechagodzilla fights back against the Alien Monsters. Lastly thanks to Mothra's energy, Godzilla revives and transforms into a much more powerful form known as "Hyper Godzilla." With the tides now turned against the Aliens, the Earth Monsters fight back and this time, with the combined strength of Hyper Godzilla, Mechagodzilla, Gfantis, and Mothra, Queen Xaxious's monsters are obliterated in an enormous explosion.
With all of their monsters gone, Queen Xaxious and Sargyle attempt to flee, but their ship is destroyed by Mothra. Sargyle is killed in the explosion, but Queen Xaxious survives and proclaims that she will destroy the monsters herself, and so, Queen Xaxious transforms into her true form: "Queen Ghidorah," a monstrous red version of Ghidorah. Once again, the Earth Monsters are unable to withstand the might of Queen Ghidorah, who easily shrugs off all of their attacks, including Hyper Godzilla's, whose strength is only at even might with Queen Ghidorah's. In the middle of the fray, Matt (whom has now repaired the X-Rider) notices that embedded into Queen Ghidorah's chest is the Scepter of Queen Xaxious, the possible source of Queen Ghidorah's power. While Hyper Godzilla is down, Matt goads him into firing at him while the X-Rider's Fire Mirror is open, and he absorbs Hyper Godzilla atomic ray into it. Finally while Hyper Godzilla, Mechagodzilla, and Gfantis manage to distract Queen Ghidorah in a beam battle. Matt manages to get in close to Queen Ghidorah and fires Hyper Godzilla's absorbed ray at point-blank at her Scepter, paralyzing her and allowing for Hyper Godzilla and Mothra to finish her off with a Nova Beam-like attack, finally ending Queen Ghidorah's threat.
With the threat finally over, Mothra and the Shobijin bid farewell, but not without expressing their gratitude to Matt for assisting them in fighting the Aliens. Gfantis too takes off back into Space, and Mechagodzilla is left to escort the remaining monsters: Godzilla, Anguirus, Varan, and Manda back home to Monster Island, while Matt and the Military express their gratitude in them for stopping the Aliens as well.
In a stinger ending, it is revealed that Zilla had survived the entire battle, but is then quickly killed by Godzilla.
- Billy Dubose as Matthew James Kennedy/"Razor Shark"
- Sarah Breidenbach as Commander Amanda Lexington
- Olivia Wolniak as Captain Kumi Wakabayashi
- James Sayson as Pilot Yuki
- Vicka Xaika as Queen Xaxious
- Jonathan R. Goldyn as Sargyle
- Jeanette Acquino as the Shobijin
- Vincent Spilotno as Vince
- Aaron Hemminger as Braddock
- Vincinza Di Franco as Enza
- Jessi Fletcher as Madison
- Joseph Flores as SWAT Team Leader
- Rosa Mendez as SWAT Team Member
- Mike Prost as SWAT Team Member
- Jenni Whipple as SWAT Team Member
- Jacob Baker as SWAT Team Member
- Jen Difatta as Sergent Lucas
- Brent Young as Kaiju Bros Team Member
- Scott Martin as Kaiju Bros Team Member
- Jeff Bean Green as Kaiju Bros Team Member
- J.D. Won as Kumi's Assistant
- Lenell Bridges as Chicago Typewriter Gunman
- Robert Scott Field as Agent M11
- Akira Takarada as the Secretary General Fuji
- Sarah Breidenbach as the Shobijin (songs)
- Miscellaneous voice provided by Sarah Breidenbach, Billy Dubose, Chris Elchesyn, Joe Flores, Megie Dekarz, and Kearstin Fay Nicholson
- Billy Dubose as Godzilla, Zombie Kong, Ebirah, and Hedorah
- Tristan Domay as Ebirah
- Kyle Jacob Baker as Hyper Godzilla, Varan, Maguma, and Slugs
- Paul Gavins as Ebirah
- J.D. Lees as Gfantis
- Riley McGee as Hedorah and Orga,
- Jeff Magnussen as Mechagodzilla III
- Scrooge Jones as Zombie Kong
- Scott Whipple as Zombie Kong
- Tommy Haire as Hedorah
- Krys Baioa as Anguirus, Manda, and Gigan
- Rich St. Andrews as Hedorah
- Nick Huber as Zigra
- Brant Morrin as Gezora
Puppetry was provided by Chris Elchesyn, Danielle Ryan, Joseph Flores, Paul Gavins, Krys Baioa, and Riley McGee.