When the arrival and intention of the fleet was certainly known and understood, by which it appeared necessary to prepare for war, Gonzalo began immediately to put every thing in proper order, and to assemble his troops; having hitherto believed himself in perfect security against any hostile attack. He appointed the licentiates Carvajal and Cepeda to be captains of cavalry, as persons in whose attachment he could confide, considering the weighty obligations they had received from him. Juan de Acosta, Juan Velez de Guevara, and Juan de la Torre were made captains of musqueteers; and Ferdinand Bachicao, Martin de Robles, and Martin de Almendras captains of pikemen. Francisco de Carvajal, who had hitherto enjoyed that office, was nominated lieutenant-general, having an hundred of the musqueteers he had brought with him from Las Charcas appointed for his guard. It was proclaimed by beat of drum, that all the inhabitants of Lima, and all strangers residing there, of whatever quality or condition, were to enrol themselves among the troops under pain of death; and money was issued to the several captains for the pay and equipment of their companies. The two captains of horse received 50,000 crowns, with which they were each ordered to levy and equip fifty horsemen; besides which, several merchants and others, very unfit for warfare, enrolled themselves. It was well known that these men were quite unfit for being soldiers; but they were constrained to enlist on purpose to exact money from them for their discharge, which in fact they purchased by furnishing horses, arms, and money to such as were in want. Martin de Robles received 25,000 crowns with which he was to enlist and equip a company of 130 pikemen. Ferdinand Bachicao had 20,000 to raise 120 pikemen; and Juan d'Acosta a similar sum for an equal number. Martin de Almendras had 12,000 crowns to raise 45 pikemen; and Juan de la Torre 12,000, to levy 50 musqueteers, who were to form the ordinary guard of Gonzalo. Antonio Altamirano, one of the principal inhabitants of Cuzco was appointed to carry the grand standard, with a troop of 80 horse; and he received 12,000 crowns for some particular purpose, as his men had no need of pay or equipments, being all chosen from among the rich inhabitants of the country.
On this occasion the several captains had standards or colours painted according to their respective fancies, the grand standard alone carrying the royal arms. Among these, Bachicao had the letters G.P. or the cypher of Gonzalo Pizarro, interlaced upon his colours, surmounted by a royal crown. Every thing being in order, posts were assigned to each officer, of which they were to take especial care by day and night. Gonzalo Pizarro made liberal donations to several soldiers who were unfit for service, as well as to those who took the field; giving them, besides what they were entitled to for their equipment, considerable sums according to their respective merits and occasions. In a general review, he mustered a thousand men, as well armed and equipped and furnished with all necessaries, as any that had been seen in the most prosperous campaigns in the Italian war. Besides their arms, which were all excellent, most of the soldiers were clothed in silken hose and doublets, and many had theirs of cloth of gold, or embroidery of gold silver or silk, with gold embroidery on their hats, their ammunition pouches, and the covers of their musquets. The army was well supplied with excellent powder; and Gonzalo gave orders that every soldier should have either a horse or a mule to ride upon during a march. In the equipment of this army, Gonzalo expended above half a million of crowns.
Besides these preparations, Gonzalo sent Martin Silveira to the city of La Plata, to bring from thence all the men and money that could be procured in that quarter. Antonio de Robles was sent to Cuzco, to conduct to Lima all the troops that were there under the charge of Alfonzo de Hinojosa, the lieutenant-governor of that city. He wrote to Lucas Martinez, his lieutenant at Arequipa, desiring him to join him immediately with all the soldiers he could raise. He sent orders to Pedro de Puelles, his lieutenant at Quito, to join him as soon as possible with all the troops from that province; and likewise ordered Mercadillo and Percel to abandon the passes of which they had the charge, bringing all their men along with them to Lima, and sent similar orders to Saavedra the lieutenant-governor of Guamanga. By these means Gonzalo exerted himself to the uttermost to collect a respectable force; and he particularly enjoined all his officers not to leave behind them any horses or arms, or any other conveniencies for those who remained to enable them to join the president. He endeavoured to justify his present conduct, by representing that Aldana, whom he had sent to give an account to the king of all that had occurred in Peru, had leagued with the president, and now employed against himself and the colony those vessels which had been confided to his charge, and which had cost more than 80,000 crowns in their equipment. He alleged that the president, who had been sent expressly by his majesty to restore peace and tranquillity to the kingdom, had raised troops of his own authority, and now proposed to come in arms into Peru, to punish all who had taken part in the late commotions, so that all were equally interested in opposing him. That no one ought therefore to reckon upon the pardon and amnesty with which the president was said to be entrusted, and which it was reported he was to extend to all who joined him; but rather that this ought to be considered as a fraudulent contrivance to divide and ruin the colonists. Even admitting the truth of the reported amnesty; it could only refer to the original opposition to the obnoxious regulations and tyrannical conduct of the viceroy, and could have no reference to those who were engaged in the battle of Quito, and the consequent death of the viceroy; as these transactions could only be known in Spain after the departure of the president, and nothing respecting them could therefore be included in his instructions and powers. Therefore, until his majesty were fully informed of the whole series of events, and had issued new orders on the subject, it became necessary to prevent the president from coming into Peru, more especially as Gonzalo Pizarro was informed by letters from Spain, that the president was not authorized by his majesty to deprive Gonzalo of the government, but merely to preside in the royal court of audience. He pretended to be perfectly assured of this circumstance, by letters from Francisco Maldonado, whom he had sent to the king, and that the president had even in some measure acknowledged this in the letter which was brought from him by Paniagua. He alleged farther, that the captains in his own employment, who had been sent into the Tierra Firma for the defence of Peru, having revolted to the president, had now persuaded him to change his tone and to invade Peru by force of arms; at which procedure his majesty would be assuredly much displeased, when informed. By these and other arguments of a similar nature, Gonzalo endeavoured to demonstrate that the president was highly to blame in detaining those persons whom he, Gonzalo, had sent to Spain, and that it was justifiable on these grounds to oppose him by force of arms. Gonzalo, by the advice of his lieutenant-general and other confidential officers, took additional measures to justify their conduct, and to satisfy the soldiers and inhabitants in the goodness of their cause. In an assembly of all the men learned in the law who were then in Lima, they arraigned the president as having acted criminally, in taking possession of the ships belonging to the colony, and by invading the country in a warlike manner, contrary to the tenor of the commission and instructions he had received from the king; endeavouring at the same time to convince the assembly, that it was just and proper to proceed judicially against the president, and those captains and others who adhered to him and abetted him in these proceedings, and that they ought to be proceeded against in a formal manner, by legal process. The persons composing this assembly of men of learning, dared not to contradict Gonzalo on this occasion or to oppose his will in any respect: A process was accordingly instituted in due form, informations taken and recorded, and judgment pronounced in the following tenor: "Considering the crimes established by the judicial informations given against the licentiate De la Gasca and those captains who adhere to him; they are found guilty and deserving of condemnation; wherefore, the said licentiate De la Gasca is hereby adjudged to be beheaded, and the captains Aldana and Hinojosa to be quartered." The other captains and officers serving under the president, were at the same time condemned to various punishments, according to the measure of guilt which Gonzalo and the leaders of his faction were pleased to charge against them; and the sentences were ordered to be signed in due form by the oydor Cepeda, and other men of letters at Lima.