Ten thousand years ago, an advanced civilization called Atlantis possessed a technology that no other civilization on Earth could ever match. To boast their scientific power, they created a species of flying reptilian creatures, called Gyaos, to eliminate the rampant pollution caused by their ignorance. However, with the extreme abundance of pollution, the Gyaos grew stronger and stronger, and started breeding so fast that the scientists couldn't keep them under control. Eventually, the Gyaos began feasting on the Atlantians themselves! For protection, an enormous species of turtle called Gamera was created to fend off the attacks of the Gyaos. The onslaught of the demons was eventually halted, and these creatures were forced into hibernation. Despite the best efforts of its people, Atlantis was ruined. So, the scientists preserved the last remaining Gamera and bequeathed him to the next civilization, so that he might protect them from the fury of the Gyaos, should they ever rise again...

The year was 1995; off the eastern coast of the Philippines, the Kairyu-Maru was trudging through the darkness of night. Its crew, and the crew of its Marine Safety escort, hoped that nothing would go wrong. The ship was carrying plutonium, and even a small leak would be disastrous. Without warning, the Kairyu-Maru ran aground on a mysterious floating atoll. The atoll moved away from the vessel and passed underneath both the ship and its escort. Fortunately, no plutonium was leaked, but the crew was shaken up, and reports of similar events started occurring throughout the area. A team of scientists landed on the atoll as it approached Japan. There, they found several small stone amulets, and a stone slab at the center of the anomalous formation. A strange writing was engraved on the slab, which was later deciphered. It revealed the names of Gamera, the guardian, and Gyaos, the shadow of evil. The atoll suddenly started to quake, and the slab was destroyed. As the scientists were thrown into the water, one was shocked to witness the giant eye and tusk of a mighty creature…

Meanwhile, three man-eating harpies, which were later identified as the Gyaos, were lured from the Goto Archipelago to a baseball stadium. With its retractable domed roof, the stadium would be the perfect area to trap and study the monsters. However, one of them escaped and flew toward the harbor, where Gamera suddenly burst from the water and knocked it out of the sky. Gamera waded through the town towards the stadium, intent on destroying the Gyaos. However, the leathery horrors escaped, and Gamera left the city to hide and gather strength.

One of the amulets found on Gamera's mighty carapace was given as a present to a young girl named Asagi Kusanagi. Through the artifact, she found herself spiritually connected to Gamera, and also discovered that she was able to bestow to the guardian the power he needed to fight his enemies.

The Gyaos found a place to hide and feed in the Kiso Mountain range, but Gamera soon arrived and saved three people from the terror of these monsters. Gamera flew in pursuit of the only remaining Gyaos, but the guardian monster was shot out of the sky by the Japanese military, whom the self-defense force saw as the greater threat. Gamera eventually escaped, but was forced to find a place to rest and gather more strength.

Meanwhile, the last Gyaos had grown to enormous proportions and was now besieging Tokyo! Gyaos landed atop the ruined Tokyo Tower, inadvertently wrecked in a military strike against the beast, making the landmark its nest. The following day, Gamera burrowed into the metropolis. It destroyed the nest and chased Gyaos across the city until the two began battling in the heart Tokyo. Gamera cut through Gyaos leg and took off into the sky, where the dazed fiend chased him into the outer atmosphere. As the two savage beasts endured the immense pressures of re-entry, Gamera ripped off Gyaos' leg and shoved himself away from the flying demon. The poor guardian crashed into an oil refinery, and the resulting explosions surrounded him with flames. Gyaos furthered the explosions with its sonic beam and landed nearby, but Gamera absorbed the raging fire and recovered! He destroyed the shadow of evil with a single massive fireball, and gave a final glance to his human companion, Asagi, as he returned to the sea from whence he came.

It wasn't long before humankind needed the assistance of the titanic terrapin once more. A shower of falling rocks from the heavens deposited a large meteor somewhere in Hokkaido. However, when the crater was found, there was no meteor. Freak "accidents" involving missing cables, electronic discharges, and high levels of oxygen culminate when a subway train in Sapporo is wrecked by a group of ravenous alien creatures, named Symbiotic Legion. As the military prepared to attack the creatures, the Symbiotic Legion constructed a massive plant-like organism in the center of the city. Because of the high levels of oxygen emitting from the flower, the military dared not strike, fearing it would cause an explosion that could engulf the city. Instead, they attacked the base of the flower, which cut off its energy flow. Suddenly, Gamera rose from the sea and soared toward Sapporo. When he arrived, he immediately inhaled all of the dangerous gases emitting from the flower. Using the oxygen as fuel, he sliced the flower from its perch with a single fireball. He ripped the remains of the flower apart with his bare hands before finishing the anomaly with yet another ball of fire.

Enraged by Gamera's attack, a swarm of Symbiotic Legions emerged from the ground and covered the turtle from head to toe. As Gamera stumbled through the city, trying to rub the hordes of human-sized alien creatures onto the buildings, the Legions mercilessly ripped and tore at his flesh. Finally, Gamera tripped over a building and fell forward. The Symbiotic Legions were suddenly distracted by nearby power transformers. Gamera awoke and lifted into the air, promptly spinning away the remaining creatures as he prepared to plunge into the sea. Following their failure at Sapporo, the Legions moved their attack south to Sendai, where a new flower was constructed that grew faster due to the warmer temperatures. Gamera arrived to destroy it, but the gigantic Legion queen knocked him out of the sky! Gamera tried desperately to keep Legion from destroying a helicopter, which contained his human link Asagi. As Gamera saved the transport, Legion opened her deadly horn and fired a devastating beam, which bored a hole straight into the guardian's shoulder. The resulting explosion stunned the monster, and Gamera was left on his hands and knees. Legion, sensing that the flower was about to launch a new mob of seeds on the unfortunate planet, burrowed out of harms way. Gamera awoke and approached the flower, careful not to trigger an explosion. Though he managed to knock the flower over to prevent it from launching a seed into space, it detonated and the city was engulfed in a massive explosion. Sendai was now a graveyard, and Gamera was lying in the prodigious crater. He appeared to be dead.

As the military tried its best to stop the Legion creatures from arriving in another city, Asagi and a group of survivors from the Sendai explosion watched and prayed for Gamera, who's outer skin had blackened and hardened. As they watched, the sparks from nearby fires began to collect above Gamera. The amulet in Asagi's hand suddenly shattered, and Gamera's body began to shake. Finally, his burnt skin fell, and Gamera was reborn. The determined reptile rose into the sky to fight Legion once more. Though the struggle between the two cyclopean gargantuans was long and difficult, the Japanese military eventually assisted Gamera by destroying the Symbiotic Legion swarm before it could attack Japan's monstrous ally. The JSDF also managed to assist by destroying Legion's shield arms. Gamera eventually ripped Legion's horn from her forehead, but she revealed a new, far more sinister attack. Legion released her laser whips, which shaved off sections of Gamera's skin and threatened to tear him apart. However, good shall always prevail against evil, and Gamera began to gather mana energy from the Earth. Legion approached the turtle with curiosity as he continued to collect the power. Finally, a plate opened in his chest and the tremendous mana beam was launched. The energy engulfed and destroyed Legion once and for all. Gamera roared out in victory and gave a final glance at the military, silently thanking them for their assistance before taking off into the morning sky.

By the end of the 20th century, the Earth's natural supply of mana, the energy that all the life forms on Earth gave off, had decreased dramatically after Gamera used the mana beam to destroy the Legion. As a result, Gyaos eggs all across the world began to hatch in mass numbers. With such an abundance of Gyaos, the creatures started breeding and eventually evolved into the much stronger Hyper Gyaos!

Meanwhile, a research team was sent out to investigate what seemed to be a graveyard of sunken ships. However, the truth was much more disturbing. Instead of finding a graveyard of boats, they stumbled upon a graveyard of Gameras! Shortly thereafter, reports of Gamera attacking Gyaos began to trickle into the newsrooms across the world. The trickle, however, soon became a flood! Finally, several Gyaos attacked Tokyo. Gamera shot one of them out of the sky over the Shibuya district of the city, converting a peaceful night into a living hell. Gamera landed, and blew up the Gyaos, as well as half of the district, with a single fireball of immense power. As Gamera brutally brawled with the remaining Gyaos, he no longer seemed to notice the humans that ran for their lives at his feet. After a bloody battle, Gamera finally rid the city of his adversaries, and flew into the sky to continue his personal war against his reprehensible relatives.

Watching with hatred, a young girl named Ayana Hirasaka, whose parents were inadvertently slain by Gamera during his battle in Tokyo four years earlier, began to share her hatred with a strange, newly hatched, creature she stumbled upon in a cave. When the diminutive demon, named Iris, attempted to use Ayana as a host to allow him to grow and gain strength, a young boy from the family who protected the cave, named Tatsunari Moribe, saved her. The creature was identified as a mutant Gyaos, and it also fit with the legend of four guardian spirits who protected the north, south, east, and west respectively. The creature broke free of its cave and grew gigantic in the surrounding forests by absorbing the life out of the people living in the nearby village.

A military strike was organized against the malicious monster, but the attack only managed to anger it. Iris lifted into the sky, and was engaged in combat by two fighter jets. The grotesque Gyaos mutation prepared to destroy the meddlesome planes when his attack was cut short. Gamera had arrived to do battle with the abomination! The two creatures fought in the skies over Japan as a typhoon passed beneath them. The military was ordered to concentrate their assault on Gamera, and the poor being was sent plummeting as Iris took his leave. The giant creature then appeared over the night's sky in Kyoto, where he sensed Ayana. Gamera soon appeared as well, and the two ancient beasts dueled in the heart of the city. Their battle eventually carried them to the Kyoto train station, where both Ayana Hirasaka and Asagi Kusanagi were located. Iris impaled Gamera on one of his spear-like arms and shoved the turtle-like monster into the station. The evil entity knocked the guardian unconscious and pushed him through to the other side of the building.

Iris had found his opportunity, and it attempted once more to merge with Ayana. Gamera, however, refused to allow such a thing to happen, and shoved his fist through Iris' stomach and grabbed the young girl. Iris impaled Gamera's hand and began to drain his energy and bodily fluids. In an act to save himself and Ayana, the noble hero severed his own hand as Iris charged two huge fireballs with the energy it drained from its opponent. While Gamera pulled Ayana out of Iris' stomach, he used what was left of his other arm to defend against the incoming fireballs. Gamera twisted and bent the fire to his will, creating a hand of flame! He rammed the blazing appendage into Iris' open belly, causing the tyrannical terror to explode. Iris' reign of evil was finally over. Gamera set Ayana near her human companions, but their attempts to save her failed. Gamera roared, and Ayana was instantly revived. She gazed at her savior, the creature whom she had once sworn to destroy, and repented of her sins.

Suddenly, reports of massive Gyaos swarms came from several different nations. It was discovered that the awful abominations were all converging on Japan! Gamera walked throw the burning city of Kyoto ready to meet them head on, as humanity, which finally realized that Gamera was an invaluable ally, prepared to join in the upcoming battle. The heroic monster and humans were linked once more, and the final battle against the shadows of evil began!