Interesting idea I just had in mind for the first sequel. Since we know it'll feature all 3 of Mothra, Rodan and King Ghidorah, you could have Godzilla temporarily turn rogue/evil by havng Ghidorah "mind-control" him the first time they meet (ideally in a new location, like in Sacramento or something) by attacking him with some kind of new special attack.
I was thinking either a Hydra Beam that injects Hydra essence of some kind into his bloodstream (which BTW, they could say that Ghidorah is the merging together of 3 Hydras instead of Dorats in this) or a Sensory EMP attack (since he obviously specializes in electrical activity) that affects peripheral activity causing him to go AWOL, either one works IMO. They could also have Mothra and/or Rodan try and disspell the control of him in a fight later on.
I think it works for a couple reasons: 1)You can get the disheartened reaction from the civilians afterwards, having them feel betrayed, which would make for a very dark sequel if they use Ghidorah right and accompany it with the right score, and 2)Ghidorah absolutely despises Godzilla and would surely love nothing more than to make him suffer as much as possible, if that means attempting to make him kill his best friend (which he could learn of their connection through their repeated echo patterns), more power to him. You could also use "he wants his archnemesis all to himself" as his motivation for doing so if you were so inclined. In any event, though, it would make their heated rivalry that much more personal in the 2nd and/or 3rd acts.
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