[1]: 175–179, 204, 216, 222 Cusco was split into factions behind Francisco Pizarro and Diego de Almagro, but these two signed a new article of agreement on 12 June 1535.

Almagro then left Cuzco, having been given the honor by Spanish King Charles I of exploring the southern part of Peru (modern-day Chile)[1]: 233–234 Gonzalo and Juan Pizarro both looked after the settlements in Cuzco, while their eldest brother Francisco explored the west coast of northern Peru and founded the city of Lima in 1535.

Manco was angered by the conduct of the Spaniards towards Incan women, especially after Gonzalo raped his queen and sister-wife Cura Ocllo.

Gonzalo set about organising an expedition in Cusco; among those he recruited was Francisco de Orellana, a veteran of the conquest of the Inca and a dependable supporter of the Pizarro brothers.

In February 1542, the leaders decided Orellana would take 50 men and continue sailing down the Napo river in search of food, then return to Pizarro.

After a brief period, Gonzalo concluded the expedition was a complete failure and decided to take a northern route back to Quito with 80 of the remaining men, unknowingly relinquishing the success to Orellana, who ended up discovering and exploring the entire length of the Amazon River.

By this time the Crown's representative, Cristóbal Vaca de Castro, had arrived in Peru amidst the confusion after Pizarro's death.

The Almagristas were finally defeated in the battle of Chupas on September 16, 1542, and their leader, Diego Almagro El Mozo, was executed.

This prompted Gonzalo Pizarro and Francisco de Carvajal to organize an army of followers with the intent of suppressing the New Laws.

Over the following months, however, the support for Gonzalo diminished when the King's new representative, Pedro de la Gasca, arrived with the intention of offering pardon and repealing the New Laws.

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