History of the end of the Inca Empire. According to history, the Inca Empire came to a tragic end when small pox and other diseases killed Huayna Capac and an estimated 2/3 of the population during the years 1524-26. In 1520, a Spanish fleet arrived at the Spanish colony at Panama carrying diseases from Europe previously unknown to the Americas. Before the Spanish arrived in Peru in 1532, these diseases had spread, eventually arriving to destroy the carefully organized Inca state. The empire then fell into a devastating civil war over Inca secession. http://ping.fm/WdQgN