After a short stay at Quito, Gonzalo learnt that the viceroy had halted at the city of Parto, about forty leagues from thence, at the frontiers of the government of Benalcazar. Resolving to follow him, Gonzalo pushed on as he had done from San Miguel, and the light troops of the hostile parties had some interference at a place called Rio Caliente. When the viceroy was informed of the approach of Gonzalo, he hastily quitted Parto and retired to the city of Popayan at a greater distance from Quito, and was pursued by Gonzalo for twenty leagues beyond Parto. As Gonzalo found that he would have to march through a desert country, altogether destitute of provisions, he here discontinued the pursuit, and returned to Quito. Perhaps this was the longest and hottest pursuit ever made in war; as, counting from La Plata whence Gonzalo first set out, to Parto where the pursuit was discontinued, the distance is not less than 700 large Spanish leagues, or 2800 miles.

On his return to Quito, Gonzalo Pizarro was so puffed up with the success which had hitherto attended him, that he frequently spoke of his majesty with much disrespect; alleging that the king would be reduced to the necessity of granting him the government of Peru, and even went so far as to say, if this favour were denied him, he would throw off his allegiance. For the most part indeed, he concealed these ambitious sentiments, pretending that he was always ready to submit to the orders of his majesty; but all his officers were satisfied that he meant to assert an independent dominion, and publickly avowed these absurd and criminal pretensions. On returning from Parto, he remained a long while at Quito, continually feasting and rejoicing; he and his adherents abandoning themselves to every degree of licence and debauchery, particularly in regard to the sex. It is even asserted that Gonzalo caused a citizen of Quito to be assassinated, whose wife he publickly lived with, and that he hired a Hungarian soldier, named Vincente Pablo to execute this infamous deed. This man was afterwards hanged at Valladolid, in the year 1551, by a sentence of the royal council of the Indies.

As Pizarro found himself in the command of a strong body of excellent troops, which appeared entirely attached to his service, some of their own accord and others by constraint, he persuaded himself that no one could oppose him, or prevent him from enjoying his present elevation in peace and tranquillity. He was even convinced that the emperor would be obliged to treat him with cautious respect, and must find himself under the necessity of entering into a compromise. It was at this time, when Gonzalo considered himself as unresisted master of all Peru, that Centeno revolted from his tyrannical usurpation in the province of Las Charcas, and that he dispatched Carvajal for the reduction of that loyal officer, as has been already mentioned.

Having continued a long time at Quito without receiving any intelligence of the measures which were taken by the viceroy, Gonzalo became anxious to learn what was become of him. Some alleged that he would return to Spain by way of Carthagena, while others gave it as their opinion that he would retire to Tierra Firma, to keep possession of the isthmus, to assemble troops, arms, ammunition, and provisions, and to wait for orders from his majesty; and a third opinion was that he would wait for these orders in Popayan, where he now was. No one suspected that he would be able to collect a sufficient number of troops in that place to enable him to undertake any enterprise for recovering his authority in Peru; yet it seemed advisable to Gonzalo and his officers to take possession of the Tierra Firma, on purpose to occupy the only direct passage between Spain and Peru. For this purpose, Gonzalo Pizarro appointed Pedro Alfonzo De Hinojosa to command the fleet which Bachicao had collected, giving him a detachment of two hundred and fifty men to enable him to occupy the isthmus, and directed him while on his voyage to Panama to coast along the province of Buenaventura and the mouth of the river of San Juan.

Hinojosa set out immediately on this expedition, dispatching a single vessel, commanded by Captain Rodrigo de Carvajal direct for Panama, with letters from Gonzalo to some of the principal inhabitants of that city urging them to favour his designs. In these letters, he pretended that he was exceedingly displeased on hearing of the violence and rapacity with which Bachicao had conducted himself towards the inhabitants of Panama, in direct contradiction to his orders, which were to land the Doctor Texada without doing injury to any one. He informed them that Hinojosa was now on his way to their city, for the express purpose of indemnifying all those who had been injured by Bachicao; and desired them not to be under any apprehension of Hinojosa, although accompanied by a considerable force, as it was necessary for him to be on his guard against the viceroy and some of his officers, who were understood to be then in the Tierra Firma levying soldiers for their master. On the arrival of Rodrigo Carvajal at a place named Ancona about three leagues from Panama, he learnt that two officers belonging to the viceroy, Juan de Guzman and Juan Yllanez, were then in Panama, having been sent to that place to procure recruits and to purchase arms, with which they were to have gone to Popayan. They had already enrolled above an hundred soldiers, and had procured a considerable quantity of arms, among which were five or six small field-pieces; but, instead of going with these to join the viceroy, they remained to defend Panama against Gonzalo Pizarro, who they expected might send a force to occupy that important station.

As Rodrigo Carvajal had only fifteen men along with him, he did not think it prudent to land in person; but sent secretly by night one of his soldiers to deliver the letters with which he was entrusted. The soldier accordingly delivered them to the inhabitants for whom they were addressed, who immediately communicated them to the magistrates and the officers of the viceroy. The soldier was taken into custody, from whom they learnt the coming of Hinojosa, and the orders with which he was entrusted. Upon this intelligence, they armed the whole population of Panama, and fitted out two brigantines which were sent off on purpose to capture Rodrigo Carvajal; but, as his messenger did not return, Carvajal suspected what had actually taken place, and set sail for the Pearl Islands to wait the arrival of Hinojosa, by which means he escaped from the brigantines. Pedro de Casaos was then governor of the Tierra Firma; and to be in readiness to defend his province against Hinojosa, he went immediately to Nombre de Dios, where he collected all the musquets and other arms he could procure, arming all the inhabitants of that place who were fit for service, whom he carried along with him to Panama, making every preparation in his power for defence. The two captains belonging to the viceroy, Guzman and Yllanez, likewise put their troops in order for resistance, and at first there was some jealousy between them and Casaos as to the supreme command; but it was at length agreed that Casaos should command in chief, as governor of the province, while they retained the immediate authority over their own men, and bore their own standards. Differences had subsisted for some time between these officers and the governor, because he had repressed some disorderly conduct in which they had indulged, and had advised them to set off with their men to the assistance of the viceroy for whom they were employed to levy troops; while they were averse from that measure, and finding themselves at the head of a respectable force, they made light of the orders of Casaos, and refused to obey him: But the necessity they were now under of providing for their mutual defence, occasioned them to enter into an accommodation of their disputes.