[2] Following the Spanish conquest of Peru in the 1530s, a few members of the royal family established the small independent Neo-Inca State in Vilcabamba, which was located in the relatively inaccessible Upper Amazon to the northeast of Cusco.

Using the justification that the Incas had "broken the inviolate law observed by all nations of the world regarding ambassadors", the new viceroy, Francisco de Toledo, Count of Oropesa, decided to attack and conquer Vilcabamba.

The group, which included his generals and family members, had then split up into smaller parties in an attempt to avoid capture.

Following this, a group of forty hand-picked soldiers under Martín García Óñez de Loyola set out to pursue them.

It was reported in various sources in 1598 that numerous Catholic clerics, convinced of Túpac Amaru's innocence, pleaded to no avail, on their knees, that the Inca be sent to Spain for a trial instead of being executed.

Many have argued that Viceroy Toledo, in executing a head of state recognized by the Spanish as an independent king, exceeded his authority and committed a crime within the political ideas of his own time.

Other claims have been made to the contrary – that Túpac Amaru was in rebellion (his predecessors having allegedly accepted Spanish authority), that Toledo had tried peaceful means to settle differences, that three of his ambassadors to the Inca were murdered and that Túpac Amaru subsequently raised an army to resist the colonial army.

An eyewitness report from the day recalls him riding a mule with hands tied behind his back and a rope around his neck.

As he did, it was reported by the same witnesses that a "multitude of Indians, who completely filled the square, saw that lamentable spectacle [and knew] that their lord and Inca was to die, they deafened the skies, making them reverberate with their cries and wailing.

"[4] As reported by eyewitnesses Baltasar de Ocampa and Friar Gabriel de Oviedo, Prior of the Dominicans at Cuzco, the Sapa Inca raised his hand to silence the crowds and his last words were: "Ccollanan Pachacamac ricuy auccacunac yawarniy hichascancuta."

Túpac Amaru's memory lived on and would become personified in an important late eighteenth century insurgency that was rooted in aspirations toward a revival of Inca status vis-a-vis the Spanish administration.

Condorcanqui's rebellion emerged in response to new Bourbon Reforms implemented by the Spanish crown, which included incremental increases in levels of taxation upon indigenous populations – such as the alcabala or sales tax.

Túpac Amaru II's rebellion was sparked when he (Condorcanqui) captured and killed the Spanish corregidor Antonio Arriaga in November 1780.

Historian El Inca Garcilaso De La Vega claimed that King Philip II disapproved of the public execution of Tupac Amaru.