The mission was nearly over. Since receiving word that Mecha-King Ghidorah was assaulting Tokyo, the Anti-Monster Defense Force members aboard the Super-X2 made plans to further their cellular fusion experiments between Godzilla's and King Ghidorah's cells, a last ditch attempt to turn the tide of the war. To do this, they would need to lead Godzilla to three special resupply bases around the Tokyo area, each housing huge amounts of spliced energy for the king of the monsters to hypothetically trigger a transformation. However, they would need to be quick - Mecha-King Ghidorah, under the influence of nameless alien invaders, was wreaking havoc in Japan's capital city and destroying precious energy reserves required to maintain Godzilla's potential new form should the need arise.
The team wastes no time, focusing their efforts on getting Godzilla to the resupply bases. One after another, the energy banks flood the giant with power, healing him from wounds received by enemy military weaponry and crumbling buildings, until at last the final base draws near. Anticipation is high as Godzilla is empowered by the final facility's energy stock. Then it happens: Godzilla's entire figure starts to pulse a black-and-purple hue, his mass increasing, his shoulders bulging into huge packs of muscle with curved spikes, green patches of glowing light forming on his midsection and the ridges of his spines, his face morphing into the scowl of his golden nemesis. And as the flashing ceases, what stands in place of Godzilla is a near-unrecognizable new being. The culmination of science and nature, the by-product of a perfect cellular fusion: Super Godzilla!
Excitement builds as the reborn king of the monsters makes his way towards the rampaging cyborg dragon, his controllers in awe of his newfound power. No monster up to this point has reached anywhere near this level of strength; it was on a totally different scale from anything Godzilla has ever fought. And now it was time to test just how strong he was. Coming into view, Mecha-King Ghidorah - previously considered equal in power to Godzilla - turns its eyes to its new foe. But before it has time to do anything, Super Godzilla pulls its fist back, encasing it in a blue light, and rushes forward with unprecedented speed! The force of the super-punch sends the three-headed terror flying away... but this would be the least of its concerns. Super Godzilla unleashes its potential: from Energy Tail Attacks, to explosive Full Body Strikes, to its orange Super Breath Attack, Mecha-King Ghidorah's health takes a nosedive. The few hits it is able to get in barely phase the deep lavender mutant, merely increasing the creature's fighting spirit. Pushed to the brink, the mechanical horror is just about finished when it is teleported from the battlefield, its alien controllers having had enough. Super Godzilla roars in victory... but is interrupted as its body begins to demorph back into its normal state! The head scientist of the Anti-Monster Defense Forces, Professor Ogata, presumes the battle must have used up all of the energy in Godzilla's body, but the loss of Super Godzilla is of little consequence. Tokyo has been saved of any severe damage, and no more monster sightings have since been reported...
Suddenly, the crew of the Super-X2 pick up the energy signal of something incredible. The invaders' trump card... A creature even more powerful than Mecha-King Ghidorah. Just as soon as its power is detected, a grotesque sphere of flesh and blood descends from the sky before Godzilla. The aliens, calling the energy body "Bagan", have it demonstrate its abilities firsthand. Instantly, the brownish-red form begins to glow a dull green, and four small orbs emerge from its sides. The body spores rapidly circle the outer edge of the pulsating mass before being launched up into the sky, one after another, and descend into the heart of Tokyo. As the four spores touch down in unison, the city lights up in a brilliant flash... and as it clears, a bloody red sky dissolves into view, revealing the horrifying truth: Tokyo has been obliterated.
Still in shock, the crew of the Super-X2 are mocked by the aliens, whom dare Godzilla to challenge their new monster to determine the fate of the planet. They then declare war on the Anti-Monster Defense Force base at the National Diet Building and fly away, the energy body in tow. Reacting quickly, Professor Ogata suggests Godzilla be led to a secret facility just outside the decimated Tokyo's city limits. Fortunately, much of the excess energy needed to transform Godzilla was moved there while the battle with Mecha-King Ghidorah was taking place. With no time to spare, humanity's last hope finds the secret facility, and is immediately flooded with massive quantities of energy. The cellular fusion is once again a success - Super Godzilla has returned.
Transformed yet again, the purple super-monster gives chase to the energy body, catching up to it near the National Diet Building. But as he nears, something within the energy body shifts... The sphere detonates in rounds of light, destroying the Diet Building and leveling other structures in the immediate area. The silhouette of a new figure fades into view: the true final form of the demon beast, Bagan! The aliens proceed to explain how they warped to Earth's ultra-ancient past to find Bagan and, using the research of Professor Ogata when he was kidnapped in a previous encounter, fused its cells with those of King Ghidorah and Godzilla, creating the ultimate monster. Despite this, both Super Godzilla and Bagan stand as equals in power. The time has come for one last battle for planet Earth.
The two super-monsters clash in a fight of epic proportions: with every attack, there is a retaliatory strike of equal or greater power. Bagan's techniques are enhanced with electricity, as are Super Godzilla's. Both beasts use everything in their disposal against one another. But as the war rages on, Super Godzilla's fighting spirit proves greater. In a final counterattack, Super Godzilla's core erupts into a concentrated stream of energy - the Nova Beam. The attack hits its mark, and Bagan's body becomes engulfed in a bright light. The legendary creature's captors can only watch in disbelief as it bellows one last time and disappears into the Earth, never to be seen again. The red sky slowly vanishes into a natural blue, and with the battle over and its energy reserves depleted, Super Godzilla once again returns to his original form, roaring victoriously. Just as the aliens are about to speed away in their mothership, the Super-X2 takes action and fires them out of the sky, bringing an end to their plans of world domination.
After his intense battle with Bagan, Godzilla's control box is destroyed, releasing the monster from human control. And as Godzilla heads back to sea under the rising morning sun, one question lingers: Upon reawakening from his deserved slumber, would the world's greatest monster return not as a savior... but as a threat to humanity?