What sixteenth-century event was most devastating the Native people in the New World?

The military invasion launched by Francisco Pizarro

The arrival of zealous Jesuit missionaries

The enslavement of native peoples on sugar plantations

The smallpox epidemics introduced by European invaders

The smallpox epidemic.

The millitary invasion was devastating but not to the extent of smallpox.

The Jesuits did not really devastate the New World.

Enslavement for sugar plantations mostly occurred with Africans.

Smallpox, brought in by the Columbian Exchange, had a widespread impact that killed a large portion of natives in the Americas.

So the Smallpox epidemic is the answer.