Here's my outline for "Destroy All Monsters": Four years after the San Francisco incident, the organization "Monarch" has been hard at work trying to find the monster Godzilla. Great debate has raged amongst the countries of the world as to what to do with the massive and powerful creature: Should the world's military might try and destroy him? Or should he be allowed to rest in peace? Things become even more complicated whenever two air force pilots in Japan, Owen Matthews & Haruko Mori, encounter a M.U.F.O. (Massive Unidentified Flying Organism), with said creature destroying Matthews' jet, and therefore killing him. The survivor of the two, Mori, is met by Dr. Serizawa in the hospital, and after hearing his account of what happened, Serizawa identifies the beast as "Rodan", the aerial equivalent to Godzilla's sea-based apex predator. But that's not all; a strange rock formation on the U.S./Mexico border is identified as a hibernating Anguirus (also identified by Serizawa). Anguirus makes his way to the West Coast, and swims for Sydney, Australia. Rodan also makes his way there. Responding in kind, Godzilla emerges in the nearby bay, and the three engage each other in battle. Rodan is driven away, and pursued by the military. Anguirus and Godzilla scuffle a little longer, but eventually drive each other away. Meanwhile, Serizawa, Mori, Dr. Graham, and Serizawa's latest associate, Miki Saegusa, become aware of the existence of a "Monster Island" that Monarch has kept secret from the public (and Serizawa) for years. The four travel to the island, where they find all manner of strange creatures gathered there (Kumonga, Kamacuras, Varan). Most important of all though, is the deity-like Mothra, who is sentient. Mothra senses trouble coming for the whole planet, a fact that the psychic Saegusa relays to the others. This trouble arrives in the form of a meteorite which crashes in India. From the meteorite comes strange creatures, which gather organic material for unknown purposes. To make matters worse, Godzilla, Rodan, and Anguirus are about to reconverge in the very area that the meteorite has landed...
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Two jet pilots, Owen Matthews and Haruko Mori (best friends ever since childhood when they dreamed about being a part of the Air Force) were on their way back to base after a flight training. Back at the base, while monitoring the two pilots, they picked up something on radar which confused them. At first, they believed it was some interference from a storm due to its massive size, but they quickly realized that it changed its course towards the pilots, following them from behind. The pilots were receiving faulty communications back from the base, but could not understand why. Then their radars showed a strange form that was right on them during their struggle flying through horrible turbulence. The turbulence subsided, and they gained control but they realized the skies got calm in an eerie way. A giant form broke through the clouds diving towards them from above, and they parted away. The giant form dived past them, which caused loss of control due to massive turbulence. They regained control when they saw that the form was way up ahead, flying towards them, a form which they made out as a giant M.U.F.O. They maneuvered away from it when the beast almost snapped at one of them. But Owen's jet was critical and could not take anymore of the strong force of turbulence caused by the beast as it flew. They tried to report back to base that they were in serious trouble and didn't know what to do, but could not get a response. The M.U.F.O. was chasing them from behind. Haruko knew that Owen was in bad shape and that the M.U.F.O. was chasing Owen. Haruko distracted the beast by shooting at it with missiles (no damage), which only caught its attention and it started chasing after Haruko. Haruko divided away from course trying to lead it the other way, so Owen could get back to base and report what had happened. Haruko got hit strong enough by one of its wings that it made his jet lose control. Haruko lead the M.U.F.O. away and Haruko tried to eject but could not. He tells Owen the situation and that he will not make it, and tells him to tell his daughter that he loves her right before the M.U.F.O. catches the jet in its mouth and the jet explodes as it is bit down on. Owen manages to get back to base where he landed, and he is sent to the hospital. After he wakes up he is met by Dr. Ishiro Serizawa, and tells him what has happened and what he saw. Serizawa is stunned to hear this and says "Rodan has awakened".
This is how I would open the movie, but I would switch Owen and Haruko around.
Stay tuned for PART 2!