The two events that weakened the Inca Empire prior to the Spanish conquest was Civil war and disease.
When the Spanish invaded the Inca Empire, they brought war which was the start of the downfall of the Inca Empire including the Aztecs and Mayans.
Disease was the main reason as to why the empire fell. There was pesticides and other things that was known to carry a lot of the diseases that spread throughout the Inca Empire and killed off the people and their crops as well.