The War of the Bloodlines
The dignitary whose task it was to fulfil the last wishes of Huayna Capac and to take his mummy to Cusco was Cusi Topa Yupanqui, who belonged to the panaca of Pachacutec and was kin to Atahualpa's mother.
When the funeral cortege reached the capital, the nobles who had traveled down were severely reprimanded by Huascar for leaving Atahualpa in the north, and were accused of conspiracy. They protested their innocence to no avail, not even confessing under torture. However, Huascar ordered anyway to kill them all, as he thought they would be dangerous enemies if he left them alive.
These events displeased the nobles who formed Huayna Capac's retinue and seemingly some of them returned to Quito without awaiting the ceremonies.
Meanwhile, Atahualpa left for Tumibamba to order the construction of a palace for Huascar, an action that displeased the curaca of Tumibamba, called Ullco Colla, who sent secret messages to Huascar complaining about the project and insinuating that Atahualpa was planning mutiny.
To ingratiate himself with Huascar, this prince sent rich gifts to Cusco, but the Inca became enraged, and killed the messengers, ordering drums to be made from their skins. After this, Huascar sent his own ambassadors to Quito with presents of women's clothes and cosmetics for Atahualpa. These episodes were the reason for a permanent rift between the brothers. Atahualpa was no longer able to return to Cusco as Huascar ordered him to do, because he would have gone to a certain death.
According to the chronicler Cobo, Huayna Capac's generals who remained in the north with Atahualpa were responsible for pressuring him to rebel, because they considered that they would be better off with Atahualpa than if they joined forces with Huascar in Cusco.
Under the circumstances, the caņaris supporting Huascar took advantage of Atahualpa's carelessness to take him prisoner, and shut him up inside a dairy shed. However, during the night, using a copper rod smuggled to him by a woman, he opened a hole in the wall and made his escape. On retelling this adventure later, he would say that the Sun god, his father, had transformed him into an amaru (snake) thus enabling him to escape.
Once free, Atahualpa went to Quito, where he collected an army to march on Tumibamba. After his victory, he punished the caņaris severely. Then he headed for the coast and, reaching Tumbes, set out to conquer the islanders of Puna, embarking in a fleet for this purpose. The people of Puna offered battle, and in the ensuing naval engagement were victorious thanks to their expertise on the water. Once Atahualpa, who had been wounded in the leg, was on dry land again, he marched non-stop to Quito. That was when the curaca of Puna attacked Tumbes and destroyed the town. On Pizarro's third trip, he found the town in that condition on arriving at the coast. He also found some six hundred Tumbes soldiers of Atahualpa's army who had been taken prisoner there.
While Atahualpa was inciting open rebellion against his brother, Huascar was busy establishing his government in the capital. By that time he had gained the support of the nobility and the ruling classes of Tahuantinsuyo. However, either he was not able to or he did not care to reinforce his prestige. His basic nature was pusillanimous, violent, cruel and whimsical. Huascar did not treat the royal ayllus in the manner to which they were accustomed, and did not attend the public banquets in the plaza, where ties of kinship and reciprocity were reinforced.
Another reason for public anger against the Inca was that he had removed from his personal guard the traditional ayllus, replacing them with Chachapoya and Caņari mitimaes, in other words, "upstarts".
After that, Huascar declared that he wanted to bury all the royal mummies and take away from the panacas all their lands, riches, servants and women. At the same time he declared that he wanted to move from the Hanan faction to that of Bajo Cusco. These events show the extent of the rift that had appeared between the sovereign and the Cusco nobility that had until then been his main ally.
Very different was the situation of Atahualpa; distance prevented him from taking part in the squabbles among the different bloodlines, and he had the firm support of his father's generals.
Huascar's loss of reputation enabled the panacas of Hatun Ayllu, to which Atahualpa belonged, to feed the fires of intrigue.
Gradually Huascar's generals began to side with Atahualpa's cause. This fact helps explain the repeated defeats suffered by Huascar's armies, despite their large number of troops. Thus, Atahualpa's generals gained ground until Huascar was left with no choice but to take over command of his troops himself.
On his side, Atahualpa was marching slowly southwards, leaving the strategy of the war to his generals. While he was in Huamachuco, he sent two emissaries to consult the famous huaca Catequil oracle on the outcome of the war. The oracle answered that Atahualpa would come to an unpleasant end. Furious, Atahualpa marched to the oracle with his golden halberd in his hand. He was met by an old priest dressed in a long white tunic decorated with sea shells. Knowing that he was the person who had made the prophecy, Atahualpa smashed his skull with a tremendous blow.
At that time news came of strange-looking white bearded people arriving in wooden houses that floated on the sea. Atahualpa remained unconcerned about those people who were visiting his dominions for the second time. On their first visit they had left before he had had a chance to see them, so this time his curiosity made him ignore his generals' recommendations to ambush them in a pass. Instead of this, the Inca offered them guides and food, and told them to proceed to Cajamarca where he was residing.
Meanwhile, Atahualpa's generals continued to defeat Huascar's troops until the Inca risked battle in a narrow pass without knowing his enemy's position. Huayna Capac's experienced generals, taking advantage of his foolish action, surrounded Huascar with their two armies. Atahualpa's triumphant troops advanced towards Cusco up to cerro Yavira. To this spot flocked the panacas and the nobles of royal lineage, forming up on either side of the huauque (the "double" or brother of the new sovereign), the Hanan Cusco on one side and the Hurin Cusco on the other, and made obeisance and paid homage to him, recognizing him as the new Inca.
After a time, a relative of the new Inca called Cusi Yupanqui arrived in Cusco with orders, according to a consensus among chroniclers, to kill all Huascar's closest kin, including his women and children, and to burn the mummy of Tupac Yupanqui. The destruction of the mummy or corpse of one's ancestor was the greatest punishment deemed possible. This revenge taken against the Capac Ayllu, to which Huascar belonged, shows that the confrontation between the two brothers was really a struggle between rival panacas.