This video explains the complicated political situations that existed once the Conquistadors subjugated the Incas, where they took the leader of the Incas hostage, but rival Inca factions initially perceived the situation as being helpful for their own interests.  The Conquistadors also broke into factions over disagreements over how their looted gold was to be distributed among themselves.  Eventually the Conquistadors killed the Incan king, but it resulted in mass unrest, where 20 - 30 rebellions ensued within the first few decades of the Spanish rule.  The Spanish undertook an aggressive policy of destroying Incan culture through forced conversion and cultural destruction, and eventually the Conquistadors fought battles among themselves to determine who would rule the area, with Pizarro ultimately being killed by Spanish attackers at his home in Lima, Peru.