In 1532, in one of the most surprising military engagements of all time, a group of 168 Spanish adventurers led by Francisco Pizarro captured the Inca emperor, Atahualpa, at Cajamarca. The emperor was with his army, in the midst of a succession war that began a few years prior upon the death of his father, Huayna Capac. As was pointed out by Charles Mann, Huayna Capac had died in a smallpox epidemic, a European import which preceded the arrival of actual Europeans in Peru. The epidemic served to destabilize the country, and was a key factor in the civil war which made it possible for the Spanish to get their foot in the door.
Still, even given those circumstances, what happened was pretty amazing. The Incan army was paralyzed due to confusion and concern over their god-emperor. Atahualpa promised a ransom of a huge quantity of gold and treasure, which he dutifully had his people collect over the next several weeks. He was executed anyway; the Spanish got involved with a successor, and the rest was history. There were several key battles, with thousands of Inca foot soldiers facing off against a mere handful of Spaniards. The Spanish never lost — the secret weapon was not gunpowder, as one might suppose, but horses, which gave them mobility and an insuperable tactical advantage in close combat. The few times the Inca were able to counter these new weapons were when they used the mountainous terrain to set ambushes and chokepoints and rockslides; kind of surprising that they did not do this more, since they lived in a country of mountains…
The Spanish rulers were kind of uneasy with the Peruvian conquest, as well as the other New World holdings won around the same time period. They were a warfaring people, but typically against the Moors; obviously a divinely sanctioned target due to their heathen nature and previous crimes against Christians. The Inca, however, had never given cause for offense, nor did they know anything about Christianity. This actually gave the Spanish plenty of room for pause, when they considered the heavenly consequences of unprovoked conquest. They finally hit upon The Requirement, a document which was read to native rulers (including Atahualpa before his capture) which basically requested a swift conversion and submission to the Church, upon pain of destruction and enslavement. Apparently, anything less than immediate surrender was grounds for whatever conquesting might follow.
The average Peruvian did not fare especially well under the Spanish; although some might make the case that the vast majority were already oppressed by the Inca overlords, or that there was basically nowhere in the world at the time where the commoner had it good. The encomienda system and the mita both turned large numbers of natives into virtual slaves. There were many defenders of the Indian in early colonial Spain, notably Las Casas, but it seemed like whenever a new system was enacted or new types of officials appointed to watch out for the Indians’ interests, they became corrupted and soon were trying to wring as much out of the Indians as ever.
One final note about the Viceroy Toledo – he just struck me so much as the villainous governor sterotype. One of his big ideas was the “reduction” of villages into towns; a forced migration of Indian communities meant to help them integrate into society. He also prosecuted the war on Vilcabamba and executed Tupac Amaru, the last independent emperor, after a sham trial in 1572; 40 years after Cajamarca.