A downed nuclear submarine and the fresh ruins of the villages of Maganote heralded the return of Godzilla, a deadly monster long dormant since his 1954 massacre. However, the Japanese government wanted proof that he was the culprit, and the Battle Cruiser Aizu was deployed on a scouting mission. For three days, the crew aboard the vessel failed to uncover even a miniscule trace of Godzilla's existence, and they were ultimately ordered to return to base. However, the creature would later emerge to do battle with the monster Baragon before traveling deeper into the Japan mainland while the SDF began to assemble their forces.

Equipped with two Satsuma submarines, the Battle Cruiser Aizu was deployed to Yokohama as Godzilla finally arrived at the defense line. After the murderous beast brutally subdued the legendary monsters Mothra and Ghidorah, the Battle Cruiser Aizu joined in an all-out assault, releasing the full force of its arsenal. Godzilla's atomic ray made short work of the resistance, and though the Aizu survived, many more were not so fortunate. The crew of the Aizu would have found themselves the next victims of the counterattack, that is, if Mothra hadn't sacrificed herself for her homeland. Her life force rejuvenated Ghidorah and the raw power of the ensuing battle sent both monsters into an intense struggle deep into the heart of Yokohama Bay. Noting a prime opportunity to gain a necessary advantage, Admiral Tachibana, aboard the Aizu, took the helm of the Satsuma and descended deep into the bay, ready to unleash the full potential of the D-03 on his old enemy...