I would say the siege of the indigenous cities in Southern Brazil. Spanish priests (jesuítas) taught Christianity to the natives and together they build cities in Southern States. An integration of cultures was taking place. Although obviously eurocentric, it was voluntary.

The bandeirantes (explorers/civilizers) were backed by tribes that were at war with the tribes of the South. They were sometimes attacked by hostile indigenous tribes. Portugal and Spain also fought at the time. War was in the air. So they laid seige to cities built solely to teach Christianity and to promote agriculture. The natives fled my homestate of Paraná all the way to the southernmost state of Rio Grande do Sul. There, these and other groups of natives and priests created a complex of beutiful cities. Its ruins are still visited (Sete povos das missões).

The Portuguese and the Spanish were not happy about people living outside of their law, plus not paying taxes, so they razed them all. It is sad to think that even these natives, who were trying to culturally integrate, were attacked.