Commander is actually from Aquabania but, unlike how the "original story" goes, he actually fled his islands when he was a young child. Too young to really remember, in fact.
(More on Commander later, he gets his own chapter.) The evil Master M knew that the Aquabanian bloodline was super-powerful and their magical traditions gave them even more strength.
He wanted this power for himself but ended out wiping out the Aqua-race as a result.
Baby Commander and some of his older relatives fled while they still could.
Commander knows very little about his heritage save stories and because they were so fantasmal he's not really sure if he can believe them or not.
But it's more fun to tell people about the Aquabats' "fantastic" origin than it is to say he and Crash started a band in high school and other people joined in over the years.
When Master M and his forces attacked Aquabania, he took many prisoners so he could to do experiments with their blood to see if he could gain their superpowers.
This resulted in many gruesome deaths. He also killed the king and queen of Aquabania when they refused to reveal to him the source of their power as a people.
Master M was not yet some great space monster, but he was a very powerful alien.
He probably could have been stopped by the Great Martian Fleet but certain loopholes within their treaty with Earth, and the fact that most native Martians loathed human Earthlings,
among other reasons, no help was to be found. (The specifics of the Martian Treaty will be discussed much later.) Master M actually used to have a body. And also a giant space army.
But after years of fighting against the super-powered Aquabanians, his army's numbers dwindled until there were few left.
Read the rest via the link in the description!