[[WMG:The puppets are alive!]]
It has been said that even though the marionette couples were separated for the night, the crew would find them together again the next morning. What if this isn't just one of those LittleKnownFacts? The only thing that keeps them from running away is their strings.
[[WMG: The puppets are controlled by Mario!]]
He fed them some kind of magical [[WhatDoYouMeanItWasntMadeOnDrugs mushroom]], and will use them to establish a new nation and TakeOverTheWorld.