You mean wiped it out with smallpox and measles viruses the Spanish explorers brought to the New World, against which the native population had no natural defense whatsoever.
Not to mention the civil war that wreaked havoc on the Inca economy and decimated the population that had survived the epidemics. The Spanish conquistadors under Pizarro were also professional soldiers with calvary (horses were unheard of in the Americas before them) whereas Vancouver's crew were not. Pizarro's crew had also not just arrived in the Americas after a 3 year journey, they were already living a comfortable life in the Spanish colony of Panama.