Nearly forty years after the conquest of Peru began with the execution of Atahualpa, the conquest ended with the execution of his nephew. A roundup of royal descendants was soon initiated by the Spanish Viceroy. Several dozen, including Túpac Amaru’s three-year-old son, were banished to Mexico, Chile, Panama and elsewhere. Some of them were allowed to return home and Túpac Amaru’s great-grandson, Túpac Amaru II, was to lead an indigenous uprising in 1780 against continued Spanish presence in Peru.

We found these kingdoms in such good order, and the said Incas governed them in such wise [manner] that throughout them there was not a thief, nor a vicious man, nor an adulteress, nor was a bad woman admitted among them, nor were there immoral people. The men had honest and useful occupations. The lands, forests, mines, pastures, houses and all kinds of products were regulated and distributed in such sort that each one knew his property without any other person seizing it or occupying it, nor were there law suits respecting it… the motive which obliges me to make this statement is the discharge of my conscience, as I find myself guilty. For we have destroyed by our evil example, the people who had such a government as was enjoyed by these natives. They were so free from the committal of crimes or excesses, as well men as women, that the Indian who had 100,000 pesos worth of gold or silver in his house, left it open merely placing a small stick against the door, as a sign that its master was out. With that, according to their custom, no one could enter or take anything that was there. When they saw that we put locks and keys on our doors, they supposed that it was from fear of them, that they might not kill us, but not because they believed that anyone would steal the property of another. So that when they found that we had thieves among us, and men who sought to make their daughters commit sin, they despised us

The five captured Inca generals received a summary trial and were sentenced to death by hanging. Several had already died of torture or disease.

The trial of the Sapa Inca himself began a couple of days later. Túpac Amaru was convicted of the murder of the priests in Vilcabamba, of which he was probably innocent. Túpac Amaru was sentenced to be beheaded. It was reported in various sources 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.

Some 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 Tupac 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. It still remains clear that he was free of any crimes since these actions, if they occurred, were in an attempt to defend against the Spaniards. The King of Spain, Philip II, disapproved of the execution.

An eyewitness report from the day recalls him riding a mule with hands tied behind his back and a rope around his neck. Other witnesses reported there were great crowds and the Sapa Inca was surrounded by hundreds of guards with lances. In front of the main cathedral in the central square of Cuzco a black-draped scaffold had been erected. Reportedly 10,000 to 15,000 witnesses were present.

Túpac Amaru mounted the scaffold accompanied by the Bishop of Cuzco. 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.” (Murúa 271)

As reported by Baltasar de Ocampa and Friar Gabriel de Oviedo, Prior of the Dominicans at Cuzco, both eyewitnesses, the Sapa Inca raised his hand to silence the crowds, and his last words were;

Túpac Amaru had left the previous day with a party of about 100 and headed west into the lowland forests. The group, which included his generals and family members, had then split up into smaller parties in an attempt to avoid capture.

Three groups of Spanish soldiers pursued them. One group captured Tuti Cusi’s son and wife. A second returned with military prisoners along with gold, silver and other precious jewels. The third group returned with Túpac Amaru’s two brothers, other relatives and several of his generals. The Sapa Inca and his commander remained at large.

Following this, a group of forty hand-picked soldiers set out to pursue them. They followed the Masahuay river for 170 miles, where they found an Inca warehouse with quantities of gold and the Inca’s tableware. The Spanish captured a group of Chunco Indians and compelled them to tell them what they had seen, and if they had seen the Sapa Inca. They reported that he had gone down river, by boat, to a place called Momorí. The Spaniards then constructed five rafts and pursued them.

At Momorí, they discovered that Tupac Amaru had escaped by land. They followed with the help of the Mamarí Indians, who advised which path the Inca had followed and reported that Túpac was slowed by his wife, who was about to give birth. After a fifty mile march, they saw a campfire around nine o’clock at night. They found the Sapa Inca Túpac Amaru and his wife warming themselves. They assured them that no harm would come to them and secured their surrender. Túpac Amaru was arrested.

The captives were brought back to the ruins of Vilcabamba and together they were all marched into Cuzco on September 21. The victors also brought the mummified remains of Manco Capac and Titu Cusi and a gold statue of Punchao, a representation of the Incan lineage containing the mortal remains of the hearts of the deceased Incas. These sacred items were then destroyed.

Following the Spanish conquest of the Inca Empire in the 1530s, a few members of the royal family established a small independent state in Vilcabamba, in the relatively inaccessible Upper Amazon to the northeast of Cusco. The founder of this so-called Neo-Inca state was Manco Inca Yupanqui (also known as Manco Capac II), who had initially allied himself with the Spanish, then led an unsuccessful war against them before establishing himself in Vilcabamba in 1540. After a Spanish attack in 1544 in which Manco Inca Yupanqui was killed, his son Sayri Tupac assumed the title of Sapa Inca (emperor, literally “only Inca”), before accepting Spanish authority in 1558, moving to Cuzco, and dying (perhaps by poison)[citation needed] in 1561. He was succeeded in Vilcabamba by his brother Titu Cusi, who himself died in 1571. Túpac Amaru, another brother of the two preceding emperors, then succeeded to the title in Vilcabamba.

The well-known Scrooge McDuck comic book Son of the Sun, written by Don Rosa, featured Manco Cápac as the original owner of various lost treasures that serve as the comic’s main plot devices, which Scrooge and his nephews are searching for.

Also in Herman Melville’s “The Confidence-Man,” first chapter, first sentence, in which Melville compares the appearance of a fictional protagonist to Cápac’s appearance out of Lake Titicaca.

Manco Capac ruled the Kingdom of Cuzco for about forty years, establishing a code of laws, and is thought to have abolished human sacrifice. The code of laws forbade marrying one’s sister, but these laws did not apply to Inca nobility and so he married his sister, Mama Ocllo or Mama Cello. With her, Manco had a son named Roca who became the next Sapa Inca. Manco Capac is thought to have reigned until about 1230, though some put his death in 1107.

Manco ruled before the title of Sapa Inca was invented, so in fact his title is Capac, which roughly translates as warlord.

In the Viracocha legend, Manco Cápac was the son of Tici Viracocha of Pacari-Tambu (today Pacaritambo, 25 km south of Cuzco). He and his brothers (Ayar Anca, Ayar Cachi and Ayar Uchu) and sisters (Mama Ocllo, Mama Huaco, Mama Raua and Mama Cura) lived near Cuzco at Pacari-Tambu, and they united their people with other tribes encountered in their travels. They sought to conquer the tribes of the Cuzco Valley. This legend also incorporates the golden staff, thought to have been given to Manco Cápac by his father. Accounts vary, but according to some versions of the legend, the young Manco jealously betrayed his older brothers, killed them, and became the ruler of Cuzco.

In one myth, Manco Cápac was a son of the sun god Inti and Mama Quilla, and brother of Pacha Kamaq. Manco Cápac himself was worshipped as a fire and a Sun God. According to the Inti legend, Manco Cápac and his siblings were sent up to the earth by the sun god and emerged from the cave of Pacaritambo carrying a golden staff, called ‘tapac-yauri’. Instructed to create a Temple of the Sun in the spot where the staff sank into the earth, they traveled to Cuzco via underground caves and there built a temple in honor of their father, the sun god Inti. During the journey to Cuzco, one of Manco’s brothers and possibly one of his sisters were turned into stone (huaca).

There are 16th and 17th century chronicles and references that support the idea of a banner, or flag, attributable to the Inca.