In reality Hinojosa, although an excellent soldier and experienced in every thing relative to warlike affairs was exceedingly ignorant in political matters. He had always believed that every thing which had been done by the insurgents was founded in justice, and that the authors of the supplications and remonstrances had a right to use their utmost efforts to succeed in procuring all that they had demanded; having even been so assured by several learned men. Yet in all the past transactions, he had conducted his own actions with much prudent reserve, so as not to go beyond the original and avowed purposes of the remonstrants, having never put any one to death or confiscated the wealth of any of the royalists, as had been done by the other insurgent commanders. On perceiving the erroneous sentiments by which he was deluded, Mexia strongly represented to him, that, as the pleasure of his majesty had been clearly expressed, by means of the commission and instructions given to the president, there was no room now to wait for any new declaration of the royal will. That all the officers and soldiers in the Tierra Firma Were resolved to obey the president, and that Hinojosa must determine without delay on the part he chose to embrace as a loyal subject, without allowing himself to be misled by these ridiculous sentiments of pretended men of learning. Hinojosa requested to be allowed one day to consider what answer he should give to these representations; and accordingly the very next day he determined to follow the advice of his friend Mexia, whom he accompanied to the president, and engaged to obey him in all things conformable to the royal orders. After this, all the captains of the troops and other principal persons in Panama were convened; who all pledged their obedience to the president, engaging to keep the matter a profound secret till farther orders. Yet the soldiers began to suspect the real situation of affairs, as they noticed that the president gave orders on every affair of importance that occurred, and that all their officers visited him very frequently, and always behaved to him in public as their superior.

As president considered that any farther delay might be prejudicial to the royal cause, he resolved to dispatch Aldana with the command of about three hundred men in three or four vessels, with orders to proceed to the port of Lima, to assemble at that place all who were well affected to his majesty. By this measure, he wished to prevent Gonzalo from having time to learn the actual situation of matters in the Tierra Firma, and from placing his own affairs in perfect order; and was in hopes likewise by these means to prevent him from putting several of the principal loyalists to death, as had been often threatened by the insurgents. Accordingly, four vessels were fitted out with all expedition, of which the command was given to Aldana, having under his orders the captains Mexia, Palomino, and Yllanez. On this occasion, in a general review of the troops, all the colours were publickly resigned into the hands of the president; who immediately restored them to the respective officers, in his majestys name, and reappointed Hinojosa as general of the army. After this, the three hundred men above mentioned were embarked under Aldana, pay and equipments, being advanced to such of the soldiers as were in need. Aldana immediately set sail on his expedition, being accompanied by the provincial of the Dominicans, a person of merit and influence, whose authority and example were expected to confirm those who might be indetermined to follow the party which he espoused. Aidaria carried along with him several copies of the amnesty and of the royal orders for restoring peace and order to Peru; and was expressly enjoined not to land on any part of the coast if possible, till he got to the port of Lima, that he might endeavour to surprise Gonzalo.

About this time, the archbishop of Lima and Gomez de Solis arrived at Panama; both of whom expressed their satisfaction on learning the turn which affairs had taken at that place, and openly declared themselves for the royal party, offering their best services to the president. At this, time likewise, the president sent Don Juan de Mendoza to Mexico, with letters for the viceroy of that kingdom, Don Antonio de Mendoza, requiring the aid of all the soldiers that could be spared from that country. Don Balthazar de Castille was sent at the same time to Guatimala and Nicaragua on a similar mission; and other persons were dispatched to San Domingo, to procure every possible assistance for prosecuting the war in Peru, if that measure should ultimately be necessary.

It has been already mentioned that Pedro Hernandez Paniagua was dispatched by the president with letters for Gonzalo Pizarro. Paniagua arrived at Tumbez about the middle of January 1547, whence he went to San Miguel, where Villalobos then commanded for Gonzalo. Paniagua was immediately arrested by Villalobos, who took from him his dispatches and forwarded them with all speed to Gonzalo at Lima, by means of Diego de Mora the commandant of Truxillo. On learning the arrest of Paniagua, Gonzalo sent a confidential person to conduct him to Lima, with strict orders not to permit any person to converse with him by the way. On his arrival at Lima, Gonzalo, in presence of all his confederate officers, restored to Paniagua his credentials and dispatches, desiring him to declare every thing that had been confided to him by his employer, and assuring him of entire personal safety in regard to every thing connected with his commission: But, if he should presume to converse either publickly or privately with any other person on any subject connected with the president, he might rest assured of losing his head. Accordingly, Paniagua boldly explained the subject of his mission. When he had withdrawn from the council of officers, some were for putting him to death, alleging that he had previously communicated his sentiments to some confidential persons. Gonzalo Pizarro did not communicate to his officers either of the two letters formerly mentioned, which were addressed to himself, by the king and the president. In this consultation, it was the universal opinion of the insurgent leaders, that they ought on no account to admit the president into Peru; many of the officers, in expressing their sentiments on this occasion, spoke of the president in a very abusive manner, and even mentioned his majesty with very little respect, at which Gonzalo seemed well pleased.

At this time, Gonzalo Pizarro wrote to his lieutenant-general Carvajal, who still remained in La Plata, directing him to come immediately to Lima, and bring thither along with him all the treasure he could procure, and all the musquets and other arms that were in that place. These orders did not proceed from any idea that these were necessary for defence, as the transactions at Panama were still unknown in Peru; but on account of the many complaints which had been made of the continual murders and confiscations which were perpetrated by Carvajal. Some alleged that he was summoned to the capital to receive deserved punishment for his cruel and tyrannical conduct; while others said it was on purpose to strip him of more than 150,000 crowns which he had amassed by pillage. At this time Lima was so entirely occupied with suspicions, that no one dared to confide in any other, or to speak a single word respecting the present state of affairs; as the slightest misplaced word, or the most trifling pretext or suspicion, was sufficient to place the life of any one in imminent danger. Gonzalo took the greatest possible precautions for his safety, of which the following is a remarkable instance. He had noticed on many occasions that the oydor Zarate was by no means attached to his interests, although his daughter was married to the brother of Pizarro: And though Zarate was sick, it was confidently asserted that Gonzalo procured him to be poisoned, by means of certain powders which he sent him under pretence of a remedy. In the sequel this rumour was confirmed by the testimony of several persons who were in the service of Pizarro at the time. Whether Pizarro were really guilty of this crime or innocent, it is a certain fact that he expressed much satisfaction on learning the death of Zarate.