Acosta caused immediate investigations to be made in regard to such as had participated in this plot, and ordered several persons to be hanged who were proved to have known its circumstances: some others in the same predicament he detained prisoners, and dissembled with the rest who had been implicated, pretending not to know that they had participated in the conspiracy: Yet, during his march towards Cuzco, he put to death several of those of whom he was suspicious, and others who endeavoured to desert. On his arrival at Cuzco, he displaced all the magistrates who had been appointed by Centeno, nominating others in their stead in whom he thought he could confide, and appointed Juan Velasquez de Tapia to take the chief direction of affairs in that city and province; and having regulated every thing to his mind, he resumed his march for Arequipa to join Gonzalo, according to his directions. In this latter part of his march, about thirty of his men deserted from him, by two or three at a time, all of whom went directly to Lima where they joined Lorenzo de Aldana. Besides these, when Acosta had got about ten leagues beyond Cuzco, Martin de Almandras abandoned him with twenty of the best soldiers of his small army, and returned to Cuzco, where he found a sufficient number of the inhabitants disposed to join him in returning to their duty, and in concurrence with whom he deposed the magistracy appointed by Acosta, one of whom he sent away prisoner to Lima, and established a new set in the name of his majesty. Finding that the number of his followers diminished from day to day, Acosta accelerated his march as much as possible, both for his own security and to serve the insurgent cause in which he was engaged. Out of three hundred well armed and excellently equipped men, with whom he had set out from Lima, only one hundred remained with him on his arrival at Arequipa. He found Gonzalo Pizarro at that place, with only about three hundred and fifty men, who a very short while before had a fine army of fifteen hundred, besides all those who were dispersed in different parts of Peru under various captains, all of whom were then under his orders. Gonzalo was now exceedingly irresolute as to his future proceedings; being too weak to wait the attack of the royalists, who continually augmented in their numbers, and yet deeming it dishonourable to fly or to endeavour to conceal himself.

In the mean time Centeno remained in the Collao, waiting an answer from Captain Mendoza to the message he had sent by Gonzalo de Zarate as formerly mentioned. While there he received dispatches from the president, which were forwarded by Aldana, and accounts of the events which had occurred at Lima, particularly the flight of Gonzalo Pizarro to Arequipa, and the junction of Acosta with the insurgents at that place. On receiving this intelligence he sent a new message to Mendoza by means of Luis Garcias, giving him an account of all these events, and particularly informing him of the orders and instructions given to the president, the general amnesty, the revocation of the obnoxious regulations, and the determination of his majesty that Gonzalo Pizarro was not to continue in the government of Peru. He apprized him likewise, that most of the gentlemen and persons of consideration, who had hitherto followed Gonzalo, had now abandoned him on account of his tyrannical conduct, in murdering and plundering all the principal colonists, and more especially because of his rebellion against the sovereign, and refusal to submit to his royal orders, and to the authority of him who had been appointed to regulate the affairs of the kingdom. Wherefore, although all that had been done hitherto might in some measure be excused, he urged Mendoza to consider that in continuing to obey Gonzalo he could no longer avoid the reproach of acting as a rebel against the king. It was now necessary and proper therefore, to forget all individual interests or past disputes, and to devote himself entirely to his majesty, to whom he was enabled by his present situation to render important service.

Alfonzo de Mendoza was already well disposed to act the part of a loyal subject in the present situation of affairs, yet uncertain how best to conduct himself for that purpose; but by this message from Centeno, he was completely determined as to the regulation of his conduct on the present emergency, and immediately declared for his majesty. By agreement between him and Centeno, each was to retain the chief command of the troops now under their orders, and Mendoza departed from La Plata with his men to join Centeno in the Collao. The union of these leaders and their troops occasioned great joy to all their followers, now exceeding a thousand men; and they resolved to march immediately against Gonzalo, taking up a position at a certain pass to prevent him from escaping, and were likewise induced to remain at that place for the convenience of procuring provisions.

At this time the whole extent of Peru from Quito to Lima had declared for his majesty. Juan d'Olmos, who commanded under Gonzalo at Puerto Viejo, on observing the vessels under Aldana passing the port of Manta in that province, had sent an express to Gonzalo giving his opinion that these vessels seemed hostile, as they had not called at the port for refreshments. He at the same time sent some Indians on board, in their ordinary rafts or flat boats, to inquire the purpose of their voyage; by means of which Indians Aldana transmitted letters to D'Olmos, urging him to quit the insurgent party, with copies of all the papers connected with the mission of the president. After perusing these papers, D'Olmos transmitted them to Gomez Estacio who was lieutenant-governor of the province for Gonzalo at St Jago de Guyaquil, usually called Culata. On learning that his majesty did not approve of continuing Gonzalo in the government, and had sent out Gasca as president, Gomez wrote back to D'Olmos, that when the president arrived in the country he should know better how to act, and might probably join him; but in the present situation of affairs, he thought it best for both to remain quiet. Juan d'Olmos went immediately to visit Gomez, accompanied by seven or eight friends, under pretence of communing with him on the state of affairs; but, taking his opportunity, one day when Gomez was off his guard, he stabbed him with his poniard, and immediately got the people to declare for his majesty, after which he did the same at his own government of Puerto Viejo.

When Pedro de Puelles, the governor of Quito, became acquainted with these proceedings of D'Olmos, and that the fleet and army at Panama had declared for the president, he became exceedingly anxious as to the measures proper for him to pursue. At this time D'Olmos sent Diego de Urbina to Quito to endeavour to prevail on Puelles to declare for the royal party. Puelles declared he was ready to receive and obey the person sent out by the king, when once he was satisfied that his majesty had no intention of continuing Gonzalo in the government, but would make no alteration in the mean time; and with this indecisive answer Urbina returned to D'Olmos. A few days afterwards, Rodrigo de Salazar, in whom Puelles reposed entire confidence, entered into a conspiracy with several soldiers at Quito, assassinated Puelles, and declared for his majesty. After this exploit, Salazar set out from Quito for Tumbez with three hundred men, with the intention of joining the president. By these several events, and others which have been formerly related, almost the whole of Peru had already returned to obedience before the arrival of the president in the kingdom.

While these favourable events were going on in Peru, the president embarked at Panama with about five hundred men, and arrived safely at the port of Tumbez; one of his ships, commanded by Don Pedro de Cabrera, being under the necessity of stopping at Buenaventura, whence Cabrera and his men marched by land to Tumbez. On his arrival in Peru, the president received letters from all parts of the kingdom, by which the writers offered him their services and assistance, besides communicating their sentiments on the situation of the colony, and giving their advice how best to proceed in reducing it to order; to all of which letters he replied with great condescension. So many flocked to his standard from all quarters, that he considered himself sufficiently strong to overcome all resistance from the remnant of the insurgents, without drawing any reinforcements from the other Spanish colonies in America; on which account he sent off messengers to New Spain, Guatimala, Nicaragua, and St Domingo, informing the governors of these colonies of the favourable turn of affairs in Peru, and that he should now have no occasion for the reinforcements which he had formerly thought necessary. Soon after his arrival, he gave orders to his lieutenant-general, Pedro Alfonzo de Hinojosa, to march with the troops to form a junction with the royalists in Caxamarca. In the mean time Polo de Menzes remained in charge of the fleet, with which he advanced along the coast to the southwards, while the president, with a sufficient escort, went by the road of the plain to Truxillo, at which place he received intelligence from all parts of the country, stating that every thing went on well.