The daunting capture of the Aztec and the Inca Empire were made possible only by a handful of Spanish soldiers and two fearless leaders. What was seemingly impossible was achieved by Cortes and later Pizzaro. These great leaders used what they had and created the situations in which they could succeed. The fall of these empires were due to three reasons: European war and weaponry advancement, Indian disorder, and most importantly invisible death caused by old world viruses.
The Europeans arrived and instilled fear in the Indians with their powerful cannons. The Indians were a Stone Age culture which had never seen such weapons of destruction. The Europeans with years of waged war had such defenses as iron suites to block the Indian revolts. The Europeans also came with what was perceived as huge deer and rode them into the war swiftly and untouched. The Indians were overpowered by the weapons the Europeans had used and tested for years of war.
The huge fall in the Indian empire by such astounding odds as that of Cortes and Pizzaro couldn't have been possible without Indians fighting against opposing tribes. Cortes could have never succeeded without the military assistance of several thousand native Tlaxcala warriors, only too happy to see the end of Aztec rule. Likewise, Pizarro's conquest of the Inca Empire in Peru which was a process that extended over some 35 years would have been impossible without the active military support of the rival Indian clans. The Native American peoples were almost always complicit in the process of conquest.
It was European, and later, African diseases that allowed the Indians to be so easily defeated. Because of their geographical isolation, the Indians had no natural immunity to Old World diseases like smallpox, tuberculosis, measles, malaria and yellow fever. Cortes conquest of Mexico in 1519 illustrates the role disease played in the European domination of the Americas.