Protoman has his Life Sword. With that he could easily take on Mecha Godzilla. Mecha Godzilla is definitely one of the toughest mecha beasts out there, but not even he can take on Protoman. Protoman is just too tough. Protoman wins.
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How? protoman is a digital program MG is a 250+ ft tall behemoth.
Don’t forget that Protoman can crossfuse. With that he can come to the human world and take down all who oppose him. Mecha Godzilla may be a strong being, but he doesn’t have enough firepower to take down Protoman. Protoman has Muramasa, the blade of fate. With it no one can take him down.