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After descending into Tokyo airspace, Varan touched down at Haneda Airport, and the J.S.D.F. and J.A.S.D.F. launched an attack against him. As Kenji Uozaki drove a truck full of gunpowder towards the kaiju, Varan confusedly watched the improvised weapon. Kenji escaped as the truck explodes, throwing Varan onto his back. Varan rose again, and the J.S.D.F. were forced to use light bombs to continue the assault as Varan flew into the evening skies.
Gaira abruptly came ashore on a cloudy day and terrorized Haneda airport. Gaira grabbed and ate several fleeing civilians, plunging Japan into a panic. When the sun finally broke through the clouds above, Gaira retreated back to the sea. Following the attack, the J.S.D.F. formulated a plan to use newly-developed Maser Cannons to kill the beast.
After defeating Destoroyah's aggregate form, Godzilla Junior reunited with Godzilla on the outskirts of Haneda Airport, near its terminals. As the monsters roared to each other, Destoroyah rose from a flaming refinery in its demonic final form, and began to fly towards the airport, bent on revenge. Destoroyah knocked Godzilla over with his Micro-Oxygen beam and grabbed Junior, carrying him high into the air. Destoroyah dropped Junior onto a building in the airport, then blasted the young monster with his beam, mortally wounding him. Destoroyah then landed on the runway and taunted Godzilla, who stormed at him in a fit of rage. After a brief skirmish, Destoroyah grabbed Godzilla by the neck with his tail pincers, taking flight and dragging Godzilla across the tarmac before loosening his grip and sending Godzilla flying into Tokyo Bay. After Godzilla came back ashore and temporarily defeated Destoroyah in downtown Tokyo, he returned to the airport and approached his fallen son. Godzilla attempted to breathe life back into Junior, who opened his eyes briefly before finally passing away. Godzilla roared in rage as his temperature continued to approach critical, when Destoroyah returned in his final form and attacked Godzilla, challenging him to a final battle.
- During filming for Godzilla vs. Destoroyah, the Destoroyah suit at one point collided with a radio pylon prop on the Haneda Airport set while being 'flown' by wires.