The Native Americans were... nearly wiped out by the arrival of the Europeans. Diseases such as smallpox swept through the tribes and killed almost everyone who contracted the highly-contagious diseases, which the Natives had no immunities to whatsoever. As if that were not enough, many Native Americans were captured and enslaved. Those not enslaved were forced away from the lands that they lived in and waged war upon when they refused to comply.
It became so bad that the Iroquois Nation had to be formed. Many of the tribes in this "nation" had been bitter enemies for centuries but banded together to face a bigger threat.
The Aztec were wiped out by the Europeans. As were the Incas.
Europeans introduced concepts of land ownership and politics that the Natives simply did not believe in. They destroyed the well-cared-for land. They wiped out 90% of some tribal populations. Finally, they created an image of the natives as savages, that has not been erased to this day.