From where Shin Godzilla left off, Godzilla remained frozen in Tokyo. Once all of his radioactive matter decayed after the stated 20 days, predicted by Hiromi Ogashira, the JSDF plans to blow the monster up in a safe manner. Supervised by Rando Yaguchi, the JSDF sends three Mitsubishi F-2 jets, armed with highly explosive MOABs. Suddenly, Godzilla emerges from the statue, with longer, bulkier arms, and a slimmer lower body. When the jets dropped the explosives, Godzilla shrugged off the damage and retaliated back with a fire of a purple spiral ray of energy, which was unlike any of his previous abilities. After shooting one of the jets, Godzilla turned his tail towards the pair of F-2s, obliterating them with a ray of his own. As a show of dominance, Godzilla's back brightened to a bright purple, until he let out a shotgun barrage of lasers down onto Tokyo, bombarding the city like he did months prior. Yaguchi and Kayoco Anne Patterson watch in horror, as Godzilla roars in victory, and he swims back into the ocean. The United States asked the UN Security Council to issue a thermonuclear strike on Godzilla. The council unanimously agreed, while the Japanese government obliged, only on the condition that the strike may be issued when the monster does not resurface on Japanese soil. When the giant resurfaced in Bikini Atoll, an island deserted since the late 1950s, two B83 warheads were launched onto Godzilla. The first was shot down by Godzilla, but the second warhead successfully made an impact. As officials, including Yaguchi, look on the atoll clearing up dust, Godzilla was nowhere to be found.
With the threat declared destroyed, the world went on as usual for the next ten years. Yaguchi was elected as Prime Minister of Japan, and he appointed Yaguchi's longtime friend, Hideki Akasaka, to become Japan's Minister for Foreign Affairs, and Patterson became the President of the United States, as a part of the Democratic Party.
In the meantime, Captain Pete "Maverick" Mitchell and Commander Bradley "Rooster" Bradshaw were doing a fly-by routine in their F/A-18 Super Hornets over the Pacific Ocean. They descend their jets down to less than 100 feet for fun, until a giant, red tail emerges from the sea. The duo pulled over just in time to not get hit and knocked over by the tail. As Rooster looked in disbelief, Maverick reported back to the USS Abraham Lincoln about the sudden emergence of a giant living object. As the giant rears its head, his mouth becomes charged with a giant bright purple light, and fires at the two. Maverick and Rooster manage to evade in time, as one of the beam's heat itself scorches parts of the canopy. Seeing it as hostile, Maverick and Rooster begin to open fire on the giant, whilst gathering footage of the creature. The creature itself didn't seem to recoil in pain, as much as it got annoyed. As Rooster contacts any nearby destroyers for assistance, with no avail, Maverick unleashes all the weaponry he has onto the creature. As the titan reared its head up for another blast of energy, a direct missile shot from Maverick into its mouth caused it to stop from charging, rearing in pain. The beast pointed its tail at Maverick. As he saw the bright light charging, he broke into a left turn before the tail opened fire with its energy beam. Unfortunately, the beam hit the left engine of the Hornet, which caused it to explode mid-air. As Maverick ejected and deployed his parachute, and Rooster watched from a close proximity, the monster flexed its back to the sky, launching a barrage of lasers that showered down to the surface. Rooster, who was narrowly hit by one, deployed his flares and successfully managed to get two laser barrages to dissipate. The monster then dove back into the sea, leaving an area of contaminated destruction.
Maverick, still drifting from the sky towards the ground, sees the giant fires on the surface of the water. Upon seeing this, he directed himself away from the fires, into an area a mile away from the inflamed sea surface. As he launches a flare for help, he sees an array of jagged dorsal plates from his right side. Looking at his compass, the creature was heading East, which meant it could possibly make landfall on Japan. A rescue helicopter spots him from the sky and picks him up, but to Maverick's surprise, his pickup crew were wearing hazmat suits, with Geiger counters scanning all over his body. As he is taken back to the USS Abraham Lincoln, he asks why the crew showed up in hazmat suits. They respond by saying how the 2016 nuclear disaster in Tokyo was due to a giant creature, which appeared eerily similar to the creature shown in the shot footage by Maverick and Rooster. When he asked what the name of the creature was, the crew simply replied, "Godzilla." Maverick repeated that word many times before he reunited with Rooster on the carrier. Waiting for him were Prime Minister Rando Yaguchi and President Kayoco Anne Patterson.
After Maverick explained the encounter with the specimen, Yaguchi concluded that Godzilla had indeed returned. When Patterson was about to translate, Maverick broke out in fluent, albeit very accented, Japanese, taking the duo by surprise. When Maverick asked about how they defeated Godzilla, they informed him of the blood coagulant that they had mass produced, which cut off Godzilla's blood supply and froze him temporarily, before he broke free from his stature. Maverick proposed a plan to inject the monster with more of the coagulant, but Yaguchi pointed out how Shin's rapid adaptation likely would render the coagulant useless. Pondering other options, Maverick recalled how the inside of Godzilla was vulnerable to conventional weaponry, citing his observations as Godzilla recoiled in plane when the missile exploded in his mouth. He proposed a solution to drop a barrage of cluster bombs into the monster's mouth, with perhaps destroying the monster from within will end the reign of terror.
Suddenly, Prime Minister Yaguchi is notified of Godzilla suddenly emerging in Toyama. As he hastily heads over to his helicopter to arrive at the National Diet Building in Tokyo, Maverick requests to fly against the monster, to assist the JSDF. Yaguchi grants him the permission, and with that, Maverick hastily asks for his F/A-18. When Rooster comes up to Maverick to ask questions, Maverick tells him about Godzilla and the 2016 nuclear disaster in Tokyo was caused by him. Asking for aircover, Rooster hops in his own F/A-18, and both jets launch off the carrier to Toyama, where Godzilla had already been wreaking havoc on the city. The JSDF try their hardest to fend off Godzilla, but all it does is annoy it. Godzilla retaliates with his heat beam, destroying most of the JSDF arsenal in one swoop. Just as Godzilla was about to finish off the last battalion of tanks that were retreating north, Maverick came in with more missiles at his disposal, and Rooster by his side. The two successfully led Godzilla back into the ocean. The duo opened fire onto Godzilla, waiting for an opening to fire Tomahawk cruise missiles from the nearby USS Leyte Gulf into Godzilla's mouth. A stray missile shot into Godzilla's eye enraged him, opening his mouth to charge up his beam. When Maverick noticed the charge-up, he immediately gave the green light to the destroyer and the Tomahawks entered through Godzilla's mouth, blowing off his head and neck. His body had flopped to the ground and his trail of destruction was over.
Just as Maverick, Yaguchi, Rooster and the JSDF were about to declare victory, the body started to rise up from where it once laid. Now the headless Godzilla roamed around aimlessly, before it started to regenerate from the neck-up. Everyone watched in astonishment, as Godzilla fully regenerated his head and neck. Instead of retaliating, however, he just returned to the sea, giving an angry look at the fiery battlefield that was the city of Toyama. President Patterson watched from the TV, as the hulking massive giant disappeared into the depths. When she arrived back in the States and told the rest of the White House that Godzilla had returned, her vice president told her to try and make use of the nuclear weapons once more. Patterson, having been anti-nuclear and pushing for the Anti-Thermonuclear Act in Congress since her first year in office to dismantle any and all nuclear warheads within the United States military arsenal, reluctantly asked the VP to garner two B61s warheads to make use.
Yaguchi, with his friend and his Minister for Foreign Affairs Hideki Akasaka, proposed a new plan with the JSDF. In the ensuing assault, Godzilla had left behind many trails of his flesh and blood, allowing for the Japanese Ministry of Education, Culture, Sports, Science and Technology to analyze samples to try and replicate the success they've had with the blood coagulant, much like ten years prior. Because they knew the coagulant wouldn't hold and destroy him permanently, Yaguchi proposed a plan that would have two pairs of fighter jets drop two waves of bombs into Godzilla's mouth. The first wave would lase Godzilla's interior and drop the coagulant directly into his mouth, preventing his heat beam from firing and temporarily freezing him. The second wave would drop a pair of B61s down his mouth, overloading his heart with the intense amount of heat and radiation and finally exploding, disintegrating his entire body and leaving no trace of him behind. When Akasaka asked who would lead the attack, Yaguchi said that an American would lead the mission.
Maverick was quarantined at a Japanese airbase for several days, because while visibly he didn't suffer from any genetic mutations or radiation burns, the Japanese had to ensure that he wasn't contaminated. Right as he was being released from quarantine, Patterson greeted him and asked him if he could lead a squadron of fighter jets to kill Godzilla. Maverick was listening, and Patterson broke down the plan to him about the new blood coagulant developing and the potential of the nuclear bombs incinerating Godzilla from within. Maverick stated how that sounded like a solid plan, but couldn't risk civilian casualties in a populated area. Rather than Maverick leading the mission and the squadron that would follow, he instead proposed that he would act as bait for Godzilla, leading the monster into an area with no human lives in danger. When Patterson asked who would lead this mission, Maverick warmly smiled at Patterson, saying that he knew someone that would be "perfect" to lead this mission.
Rooster, who was still onboard the USS Abraham Lincoln, was approached by Maverick. After rhetorically asking whether he was clear of any radiation, Maverick proposes to Rooster about the plan that Patterson wanted. When Rooster asked why he cannot lead the mission, Maverick told him that he would bait Godzilla. Rooster, feared of losing his father-figure, wanted Maverick to not take the risk, but Maverick warmly smiled at him too, telling him that the world was at stake if Godzilla was not stopped. He then tells Rooster that he has faith in him to lead the world to victory.
Two weeks have gone by without Godzilla making landfall. Satellites were able to detect when he had ventured close to the Japanese mainland. During this time, Maverick and Rooster break out the plan to Rooster's longtime wingman, Commander Jake "Hangman" Seresin, and two volunteers from the Japanese Air Self-Defense Force: Lieutenants Takao "Yamato" Honda and Michiru "Kiryu" Tezuka. Dubbed "Operation Hokmuto," the plan would have Godzilla being redirected by Maverick and a fleet of naval destroyers to the northwest side of the Sea of Japan, to ensure any human civilians wouldn't get affected by the possibility of a nuclear explosion, but also if the nuclear explosion happens, it wouldn't interfere with the ring of fire under the depths of the ocean. The first wave would have Rooster and Hangman lase Godzilla's mouth and launch the coagulant bomb into his mouth, pulling up right before he freezes. Right as he freezes, a second wave of a pair of Japanese F-35s would lase and drop two B61s into Godzilla's mouth, overloading him with nuclear energy before his internal reactor eventually collapses and explodes, and his body with it. By this time, Yaguchi had received word that the coagulant had finished producing the necessary amount for this mission. Due to the backing of the government, the coagulant was ten times faster at freezing Godzilla's blood traces than ten years ago. The amount necessary was compacted into two bombs that were shaped like GBU-12s.
Godzilla was detected to have been drawing closer to Niigata. The five pilots are transferred to Chitose Air Base, where Yaguchi gives one final encouraging speech about the future of Japan and the world, after killing Godzilla. Maverick gives one final call to his wife, Penny Benjamin, before he hops on his F/A-18. Suddenly, satellite images pick up Godzilla breaching the surface, and that is when Maverick is launched to lead Godzilla to the Sea of Japan. With limited munition and fuel, he puts a picture of him and Rooster on his right side before charging his jet towards the resurfaced Godzilla. Annoying him with bullets and barrage of missiles, he successfully leads Godzilla away from Niigata, where destroyers miles ahead open fire to draw his attention. The chase goes on for several hours, with Godzilla stopping momentarily to fire at the sky and at the destroyers. In the span of those hours, five destroyers were struck and sunk by Godzilla's atomic barrages, whether from his mouth, tail or back. But Maverick survived long enough for him to reach the checkpoint. As he opened fire in all directions, circling around Godzilla's upper body to keep him in his place, Maverick climbed to the altitude where Rooster and Hangman were circling around the area minutes beforehand. Godzilla opened his mouth towards the sky preparing to charge for another attack. Just as it was ready to fire, Maverick gives the signal to attack, and Hangman successfully lases Godzilla's innards for Rooster, dropping the coagulant bombs inside of his body.
As they perform a high G climb to avoid crashing into Godzilla, Godzilla's breath stops charging but he still turns around to prepare some sort of assault. From the end of his tail, a flock of Godzilla humanoids emerged and sprouted wings, gaining at the three. Godzilla's back shoulders split open to unveil a pair of wings, as the three Hornet pilots, as well as Yaguchi watching the situation with the Cabinet, stare in absolute shock. Just as Godzilla was about to launch himself to fly, the wings started to crumble. The coagulant was starting to work and was trying to freeze over his body. However, Godzilla's adaptation was allowing him to fight back against the freezing process, but he could not attack the jets. While the Super Hornets were fending off against the horde of flying mini-Godzillas, the two F-35s finally arrived at the scene from the air base. Because Godzilla was reeling and shaking his head in all directions, for he was in pain from the coagulant taking his body over, the pair could not get a clean shot in. With another horde of flying Godzillas heading their way, the F-35s opened fire with their missiles and guns. With Godzilla being aware that he would be frozen again, he attempted a last minute attack. He resprouted his wings and faced them and his back towards the sky, launching a ball of energy into the sky. The ball slowly broke apart into different lasers that were raining down from the sky, destroying several more destroyers in the Sea and almost hitting the squadron of F/A-18s and F-35s. Maverick wasn't so lucky, as he was struck by the laser barrage from the sky. Just as his jet crashed into the sea, he shouted into comms for the F-35s to regroup and attack Godzilla, before his radio went dead.
Motivated by this, the F-35 pair finally charged at Godzilla, and then performed a high G climb for Godzilla to face up towards them. Godzilla's mouth brightened to another purple, but the coagulant was already starting to take a toll on his atomic energy. Being unable to unleash his weapon, the F-35s lased onto Godzilla's interior with the B61s and dropped them. They then entered his body, forcing the F/A-18s and F-35s to retreat from the area. As Godzilla roared in sheer defiance, his body lit up and a giant mushroom cloud formed in the water. All four of the jets' canopies were shaking, with one of Rooster's engines malfunctioning and shut off by the shockwave of the blast. The horde of humanoid Godzillas that followed them couldn't catch up and were incinerated in the blast. Visual satellite images have shown that there have been no traces of Godzilla's remains, ensuring his death once and for all. Suddenly, a flare was shot from the sea. When Rooster descended down, it was Maverick, who parachuted far enough to not suffer any burns from the nuclear explosion. Rooster radioed the USS Abraham Lincoln, to send a rescue chopper for Maverick.
They all gather back in Chitose Air Base, where the five pilots hug it out for saving the world from Godzilla. Yaguchi and Patterson were there, and Maverick saluted the two, as they thanked him for his service. The film ends with Maverick being awarded the Medal of Honor by President Patterson, and Maverick motorbiking back to his home in San Diego to his wife and stepdaughter.