After the appearance of a new Godzilla in 1999, the JSDF began a program to convert the skeletal remains of the first Godzilla into a battle cyborg. The AC-3 "Shiragasi" would be the new high tech aircraft designed to carry and deploy, transmit energy to refuel, remotely control, and provide extra fire support for Kiryu, the Mechagodzilla. In 2003, when the JSDF was unveiling Kiryu, the new Godzilla made landfall once more. Caught off guard, the Shirasagis transported Kiryu to the scene of battle in record time. Godzilla ceased his advance the very moment he caught sight of his metallic mirror image. As the jets hovered in standby phase, Kiryu attacked its quarry. As Kiryu was preparing to fire its ultimate weapon, the Absolute Zero Cannon, Godzilla roared. Kiryu malfunctioned and its chest mounted cryoweapon refused to fire, allowing Godzilla to escape.

The Shirasagis attempted to rendezvous with the cyborg, but Kiryu suddenly lashed out with one of its wrist-mounted laser cannons. One of these aerial support vehicles barely managed to escape. Godzilla's roar had awoken the memories of the first Godzilla, that chaotic entity of fifty years prior. Making its way deeper into the city, Kiryu destroyed everything in sight. One Shirasagi flew around Kiryu in an attempt to lure it away from the metropolis, only to be repelled by Kiryu's mouth-mounted maser cannons. When the cyborg turned its attention back to its errand of terror, one of the pilots courageously (yet recklessly) attempted to divert the cyborg's heat seeking missiles. The berserk mechanical beast didn't even acknowledge this act of heroism. Fortunately, the crew members were rescued before their cutting edge vessel erupted into a fiery explosion.

In the dead of night, Godzilla began an assault on Tokyo. The order was hesitantly given to deploy Kiryu once more, and the Shirasagis unleashed their mecha in midflight, allowing it to body slam Godzilla before the dreadful monster could annihilate evacuating civilians. The battle between monster and machine resumed and when it had appeared as though Kiryu had gained the upper hand, it readied its Absolute Zero Cannon once more. Godzilla, proving his remarkable knack for escaping destruction just in the nick of time, regained consciousness at that very moment. A powerful atomic blast emanated from the reptile's maw, causing Kiryu to topple over and fire its weapon in a rogue direction, accidentally demolishing several buildings. The situation became very grim when Kiryu exhausted its energy supply. Soon, the Anti-Mega Losses Force ordered nearby power plants to divert all energy to their headquarters. Tokyo experienced a massive blackout. One of the Shirasagis transferred power from home-base in an attempt to transmit energy to Kiryu, while the others provided backup for the Type 90 Maser Beam Tanks. Kiryu rose, only to be blasted by the might of the monster king. When Godzilla's mechanical doppelganger rose once more, one of the Shirasagi pilots witnessed a horrific sight; Godzilla's dorsal plates began to flicker and glow, a precursor to that insidious death ray that could effectively end Kiryu's last-ditch effort to charge and fire its Absolute Zero Cannon. The copilot was ejected and the pilot fired at Godzilla, turning the creature's attention to the warplane instead. The aircraft's wing was torn asunder by the searing hot plasma, and the Shirasagi crashed directly into Godzilla's mouth! Having fully charged, Kiryu ignited its rockets and slammed into Godzilla. Kiryu grabbed the fighter's remains and hurled them into the sky, allowing the pilot to safely eject from the doomed vessel. Grasping Godzilla's mouth, Kiryu and its fleshy foe crashed into the ocean. A giant ice crystal formed and shattered; the Absolute Zero Cannon had fired. Alas, Godzilla was only injured. The once unstoppable monster bid a hasty retreat as Kiryu rose to the surface, its reserves exhausted.

Less then a year later, Godzilla began his assault anew on Tokyo. Heading for Kiryu's home base, enraged by mankind's affront to his forebearer's remains, the nuclear leviathan was caught unaware by an aging Mothra. The battle lasted long into the night before the all clear was given to send Kiryu into the fray. The battle raged on as Mothra's larvae joined the battle. Eventually, Mothra passed on and Kiryu was knocked out of commission. The Shirasagis offered fire support to the twin Mothra larvae while one of Kiryu's maintenance workers attempted to complete the monumental task of bringing the mighty hybrid of carbon and silicon back online.

Upon repair, Kiryu made its way to Godzilla and delivered a critical blow with its drill hand and Triple Hyper Maser Cannon, allowing the larvae to encase the raging saurian in silk. When Kiryu was ordered to deliver the finishing blow, it refused. Godzilla's distress once again awoke the 1954 Godzilla deep within Kiryu, and the mighty machine began to transport Godzilla to the sea. One of the Shirasagis followed in order to free the trapped maintenance worker, and curiously, the cyborg seemed to be aiding in the human rescue all along. Using a computer monitor to bid its final goodbyes, Kiryu crashed into the ocean with Godzilla in tow, but not before the trapped human was freed from the machine. The pilot of the Shirasagi ejected to rescue him, and they parachuted safely to the sea. Meanwhile, one of the remaining jets arrived to transport them home. With Kiryu gone and Godzilla defeated, the future of this fleet of workhorse aircraft remained uncertain.