Well the Native Americans also didn't really realize the intent of the Europeans and were too decimated later on to drive them into the sea. It wasn't like Amerindians didn't have the power, they just didn't have any concept of what was going on and let the Europeans get entrenched. A similar thing happened in Mexico when all those tribes destroyed the Aztecs - they didn't realize that the strangers who got them to do it were going to come enmasse and enslave them all. South America was decimated by civil war so they weren't able to do too much against dick Spaniards killing their king.
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