It was soon learnt that Gonzalo received regular advices of ever thing that occurred, and great care was likewise taken by Aldana to procure intelligence of all that passed in the camp of the insurgents; so that every day messengers went and came between both parties, and both were continually endeavouring to mislead each other by false reports. Accordingly it was reported one day that Gonzalo and his troops Were in full march for Lima, which occasioned much confusion and dismay in that city; but it was known afterwards that this rumour had been purposely spread by Gonzalo and his lieutenant-general, on purpose to prevent Aldana from pursuing them, a measure of which they were much afraid. In this unpromising state of his affairs, great numbers of the adherents of Gonzalo abandoned him, believing that he could not resist the power of his enemies. Such of them as had horses took the road to Truxillo; and all the rest endeavoured to reach the ships of Aldana, concealing themselves as well as they could in retired places till they might ascertain that Gonzalo had proceeded farther on his march, which indeed he continued to do with much precipitation. When he had proceeded to a considerable distance from Lima, all those who had abandoned him flocked to that city, and every day some fresh deserters came there, by which means Aldana got accurate intelligence of the proceedings of Gonzalo, who was reported to be in continual dread of being put to death by his own men. After the flight of the licentiate Carvajal and Gabriel de Roias, Gonzalo made no farther use of the royal standard, only displaying that which contained his own arms. His cruelty increased with his disappointment, insomuch that not a day passed in which he did not put some one to death. He took extraordinary precautions for his own personal safety, which were so far effectual, but every effort to prevent desertion was unavailing.
Lorenzo de Aldana sent intelligence of all these matters to the president, by means of messengers dispatched both by sea and land, earnestly urging him to come into Peru as quickly as possible, as the insurgent party seemed at so low an ebb that nothing was wanting but his presence to make it fall entirely in pieces and submit without a struggle. On the 9th. of September 1547, when assured that Gonzalo had retreated eighty leagues from Lima, Aldana landed with all his officers and all the inhabitants of Lima that had taken shelter on board his ships. He was received on shore with every demonstration of joy and respect, every one who was able appearing in arms to do him honour. Having appointed Juan Fernandez to the command of the ships, he took charge of the vacant government of Lima, where he made every possible preparation for carrying on the war, collecting arms ammunition and all other necessaries.
Some time after the departure of Juan d'Acosta from Lima for Cuzco by the mountain road, as already mentioned, at the head of three hundred men well armed and equipped, he got notice that Gonzalo Pizarro had abandoned that city; on which he sent Fra Pedro, a monk of the order of Mercy, to Gonzalo, to demand instructions for his ulterior proceedings. Pizarro sent back the monk with directions for Acosta to join him at a certain place. On his return to Acosta, accompanied by a person named Gonzalo Muquos, after delivering his dispatches, Friar Pedro gave him an account of all that had happened in the army of Gonzalo, and in particular of the great number of men that had deserted from him; which Acosta had not before learnt, though several of his soldiers had received the intelligence by letters brought to them by the Indians who frequented the camp, but which they dared not to communicate to each other. On the present occasion, the messengers from Gonzalo recommended to Acosta to keep this matter as secret as possible till such time as he should join Gonzalo. Acosta therefore, gave out that he had received favourable intelligence from the monk, and that Gonzalo had been successful on several occasions, being daily joined by many additional soldiers; and, as he had found it convenient and necessary to send off many confidential persons in various directions, these persons pretended to have deserted from Gonzalo by way of stratagem, on purpose, to gain possession of the ships commanded by Aldana. All this however was insufficient to disguise the truth from many of the followers of Aldana, particularly Paлz de Sotomayor, his major-general, and Martin d'Olmos one of his captains; who, coming to a knowledge of the real state of affairs, entered into a resolution of putting D'Acosta to death. They formed this resolution unknown to each other, as no one at this time dared to avow his sentiments to any other person, for fear of being put to death; yet, from certain indications, they began to suspect each other of entertaining similar sentiments, and at length opened themselves reciprocally, and communicated their purposes to several soldiers in whom they confided. Just when they were about to have put their enterprize into execution, Sotomayor got notice that D'Acosta was holding a secret conference in his tent with two of his captains, and that he had doubled his ordinary guard. From these circumstances, Sotomayor concluded that their conspiracy, having been revealed to several persons, had been betrayed to Acosta. He took therefore prompt measures to inform all his confederates, and both he and they took horse without delay, and left the camp in sight of all the army, to the number of thirty-five in all; among whom, besides Sotomayor and D'Olmos, the principal persons were Martin d'Alarzon who carried the grand standard, Hernando de Alvarado, Alfonzo Regel, Antonio de Avila, Garcias Gutierrez d'Escovedo, and Martin Monje; who, with all who went off on this occasion, were men of consideration and of much experience in the affairs of Peru. These men took immediately the road for Guamanga, and used such expedition that, though Acosta sent off sixty mounted musqueteers to pursue them, they made their escape in safety.
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.