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Level 1: Osaka
A horrible three headed dragon, dubbed King Ghidorah, is leveling the city of Osaka. No weapon of man can stop the creature, so the fate of Earth falls upon the hands of a few. Together, a scientist and a few others gain control of Godzilla and send the leviathan out to stop the terror. Followed closely by the Super X2, Godzilla must wad through the crumbling city to face Ghidorah, who either lies at Osaka Castle or Tsutenkaru Tower. Can the newly turned defender of the world eliminate the golden beast?
Boss:

Level 2: Mt. Fuji
After blasting free King Ghidorah's central head, the monster is teleported away. It is shown to the astonished world that the dragon was the tool of an invading alien race. The celestial beings warn mankind that they will fall.and that they have only begun to see their true power. Meanwhile, a new enemy has arisen. Mankind moves Godzilla to the forest ridden mountains, but is astonished to find what is awaiting them. Another Godzilla is here. Which is truly the real Godzilla?
Boss:

Level 3: Lake Ashino
On the mountain, it is revealed that the fake Godzilla is a robot in disguise. Once the truth is shown, it does not take the monster long to eliminate his steel clone. Though during the battle, the aliens have now kidnapped the professor. The beings hid the man in one of several locations, and it is Godzilla's job to find him. Time is running out for Godzilla. Can the giant find the professor, and defeat the beast that dwells in Lake Ashino? Only time will tell.
Boss:

Level 4: Yokohama
Godzilla rescues the doctor, and dispenses with the plant hybrid, Biollante. In return, the professor injects some King Ghidorah cells into Godzilla, thereby making him stronger. The experiment proves successful, and just in time. A new monster is flying around Yokohama. A deadly insect like bat creature called Battra. Godzilla must face against a foe that can dodge nearly all his attacks. And, to make matters worse, another Battra, in larva form, is cocooned. Can Godzilla defeat the buzzing mutant, and stop the birth of another?
Boss:

Level 5: Tokyo Part 1
In the end of the battle, Godzilla kills both of the Battras and ventures to the final site of conflict. The aliens have tempted man with a choice. Godzilla could either seek out the 5 energy capsules that would turn the reptile into Super Godzilla, or stop Mecha-King Ghidorah before 50% of the city burns. Which choice will lead to victory, and which would lead to the end of Earth? Is Godzilla strong enough to destroy Mecha King Ghidorah, or does Super Godzilla have to stand up to the plate?
Boss:

Level 6: Tokyo Part 2

Whichever choice you make, Godzilla proves the victor. But all is not well as a huge twisting ball of flesh and blood descends, heralding several spores of its matter leveling everything in site. The aliens proclaim that Bagan, a creature from Earth's ancient past, has been injected with cells from Godzilla and King Ghidorah making it the ultimate warrior. Godzilla must now face the demon, and stay alive long enough for the Super X2 to retrieve the necessary energy for Godzilla to transform into Super Godzilla. One side will fall..which side?

Boss: