Given that the Nopon Archsage is essentially the fanbase's Audience Surrogate, perhaps he could bring all of the series' characters together to fight it out, while that plan goes awry due to one of the series' main villains trying to hijack that plot to destroy all of existence.
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It has become a common guess to the point of becoming a joke in the fandom, but it'll be said here anyway. As the Xenoblade series has become a meteorically rising star for Nintendo, a Dynasty Warriors collaboration as has happened with Zelda and Fire Emblem would make sense to ride the hype.