Warmatrix

Spanish conquistadores attacking Inca workers

Like the earlier defeat of the Aztec empire, the taking of Tawantinsuyu, the Inca empire, was an astounding feat of conquest. The latter was the most difficult of the two; the Aztec empire was brought down in two years, the Inca in seven. The tiny band of Spanish conquistadores that accomplished it succeeded because it was helped by two external factors: Inca infighting and disease.
Francisco Pizarro, his four brothers and others had made reconnaissance missions into South America in 1522 CE, 1524 CE and 1526 CE. During the last they made contact with the Inca. Francisco Pizarro, Diego de Almagro and Hernando de Luque returned to Spain and got permission from the king and queen to conquer the empire, though nobody knew how large or strong it exactly was. Pizarro returned in 1531 CE with 168 men, 1/3 cavalry and 2/3 infantry. Facing them was an empire with an estimated population of about 16 million.
But the Inca had contracted a disease from the Europeans, possibly smallpox and/or measles, which raged through the empire. One of its victims was emperor Huayna Capac, in 1528 CE. Upon his death his sons Atahualpa and Huáscar started a civil war for the throne. Atahualpa had his power base in the north and was supported by the greater part of the army; Huáscar occupied the south, including the capital Cuzco, and had the priests behind him. In 1532 CE Atahualpa managed to defeat his brother in two large battles. On his way to Cuzco, he met Pizarro and his band at Cajamarca.
Atahualpa had been informed about the Spanish and had trouble deciding if they were gods, devils or just ordinary men. Pizarro, through his lieutenant Hernando de Soto, invited him to meet at the plaza of the town. The emperor, curious, showed up with 6,000 courtiers, mostly unarmed. The Spanish launched a surprise attack, massacred 2,000 Inca and took the emperor hostage. Atahualpa tried to buy himself free with an entire room full of gold and silver. The ransom took a few months to gather, then the Spanish killed their captive anyway. The Inca empire, a centralized state, was now decapitated.
The conquistadores split up into two groups, one heading north and the other under Pizarro south towards Cuzco. Both were joined by rebellious tribes who had been conquered by the Inca earlier. There were several battles along the road and each time the nucleus of terrifying Spaniards, together with their allies, were victorious. Pizarro installed Atahualpa's brother, Tüpac Huallpa, as a puppet, but he died soon after and was replaced by Manco Inca Yupanqui, who at first allied himself with the Europeans. Spanish and Inca together defeated the northern armies of Atahualpa and then made themselves master of Cuzco, the heart of the empire.
Early explanations for the victory of the Spanish conquistadores included a supposed awe of the Inca for the invaders and superiority of the Spanish weapons (plate armor, gunpowder weapons and horses), however these seem to have been minor factors. The conquistadores brought with them experience and superior tactics from the Old World, but the Inca were quick to adapt, as they demonstrated in the Battle of Vilcaconga. Far more decisive were the civil war and the epidemics, both of which seriously weakened the empire just before the arrival of the conquistadores. The infectious disease(s), striking in five waves, are estimated to have killed 93% of the Inca population in just half a century.
After Cuzco, Pizarro went off to find more gold. In his absence two of his brothers treated Manco Inca Yupanqui so badly that he rebelled. He fled Cuzco though returned in 1536 CE with an army to recapture it. 190 Spanish and several thousand Inca warriors defended the city against an army of maybe 40,000 men. The Siege of Cuzco lasted almost a year and saw the Spanish and their allies hard pressed. When reinforcements led by Diego de Almagro finally turned up, the Inca emperor withdrew to Vilcabamba and established a neo-Incan empire. This consolidated Spanish rule over most of Inca territory, or Peru, as they called it.
Later Pizarro and de Almagro fell out with each other and fought a civil war of their own. Pizarro won, but was later killed by supporters of de Almagro. In the meanwhile more and more Spanish arrived, the city of Lima was founded as a new capital and a full colony was established. The neo-Inca empire held out for 35 more years. In 1572 CE Francisco Toledo arrived, the first viceroy of Peru. He declared war on the remaining Inca. The last emperor Túpac Amaru was killed, the new capital Vilcabamba sacked and its inhabitants relocated to another town.