Leaving Quito, Carvajal went, directly to San Miguel, where the principal inhabitants went out to meet him, and conducted him with much respect to the house which was prepared for his reception. On arriving there, he desired six of the most considerable persons belonging to the city to dismount and accompany him into the house, under pretence that he had something of importance to communicate to them from the governor. Having caused the doors to be shut, and posted centinels to prevent any communication with the rest of the inhabitants, he represented to these men, that Gonzalo was much incensed against them for having always taken part with his enemies, and more especially on account of having received and favoured the deposed viceroy, and of having readily supplied his army with every thing of which they stood in need. On this account it had been his first intention to have destroyed the city with fire and sword, without sparing a single inhabitant. But, on reflecting that the magistrates and principal inhabitants only were to blame, the people at large having been constrained by force or fear, he was now determined to punish only the most guilty and to pardon the rest. Yet, having certain private reasons for dissembling for the present with some of the principal persons of the place, he had selected the six who were now present, as principal inhabitants, to punish them as they richly deserved, that they might serve as a warning to all Peru. For this reason, therefore, he desired them to confess their sins in preparation for death, as he was resolved to have them all executed immediately.

They used every argument to exculpate themselves from the crimes kid to their charge, but all they could say was without avail; and Carvajal even caused one of them to be strangled, against whom he was particularly incensed, as he had been principally instrumental in constructing the royal seal which the viceroy employed in his dispatches. In the mean time, a rumour of what was going forward at the residence of Carvajal spread over the city, and came to the knowledge of the wives of the prisoners. These ladies immediately implored the priests and monks who dwelt in San Miguel to accompany them to the place where their husbands were in so great danger. They all went there accordingly, and got in by a private door which had not been noticed by the people belonging to Carvajal, and which had consequently been omitted to be guarded. Coming into the presence of Carvajal, the wives of the prisoners threw themselves at his feet, and implored mercy for their husbands. He pretended to be softened, and granted pardon to the prisoners, so far as their lives; yet reserving to himself to punish them in such other manner as he might see fit. Accordingly, he banished them from the province, depriving them of their lands and Indians, and condemned them in the payment of heavy fines towards defraying the expences of the war.

From San Miguel Carvajal went to Truxillo, collecting every where on his route all the soldiers, horses, arms, and money he could find. Carvajal had resolved to have put one Melchior Verdugo to death, who dwelt in Truxillo; but as Verdugo got intimation of this intention, he fled to the province of Caxamarca, where his repartimiento of Indians was situated. The bussiness on which Carvajal was engaged was of too great importance to admit of pursuing Verdugo; wherefore, after having got possession of as much money as possible under pretence of a loan, he went on to Lima, always collecting all the soldiers he could procure. He gave no money to his recruits, only supplying them with horses and arms, which he took wherever they could be found. He kept all the money he could find for his own use, every where pillaging the royal coffers and public funds, and even searching for treasure among the ancient tombs. After arriving at Lima, he completed his military preparations, and departed for Cuzco by way of the mountain and the city of Guamanga, at the head of two hundred men well equipped, and carrying with him a great sum of money which he had collected during his march; and at Guamanga he conducted himself in the same rapacious manner as in other places.

Seven or eight days after the departure of Carvajal from Lima, a conspiracy was detected among those who were well affected to the royal cause, in consequence of which fifteen of the principal persons of that city were committed to prison. Among these were, Juan Velasquez, Vela Nunnez nephew to the viceroy, Francisco Giron another gentlemen of his household, and Francisco Rodriguez. By means of the torture, these unhappy persons were made to confess that they had concerted with Pedro Manxarres, an inhabitant of Las Charcas, to kill the lieutenant-governor Aldana, the provost marshall Pedro Martin, and other friends and partizans of Gonzalo Pizarro, after which they proposed to induce the citizens of Lima to declare for his majesty, confidently expecting that all those who now followed Carvajal by constraint would join their party; and they intended finally to have gone off with all the strength they could muster to join Centeno. Upon this forced confession, Giron and one other of these prisoners were strangled. By the intercession of several respectable persons the life of Juan Velasquez was spared, but his right hand was cut off. All the rest of these prisoners were so severely tortured that they continued lame for the rest of their lives. Manxarres saved himself by flight, and continued to conceal himself among the mountains for more than a year; but fell at last into the hands of one of the officers in the interest of Gonzalo, who caused him to be hanged.

As Pedro Martin, the provost-marshal, strongly suspected that some of those who accompanied Carvajal had participated in this plot; he endeavoured to discover this by torturing Francisco de Guzman, one of the prisoners. Finding that Guzman made no confession on this head, he interrogated him particularly respecting a soldier along with Carvajal named Perucho de Aguira, and some of his friends, demanding to know whether these men were in the secret. On purpose to free himself from the torture, Guzman said they were. After this confession, Guzman was formally condemned to become a monk in the convent belonging to the order of mercy, in which he accordingly assumed the habit. After this, Martin demanded from the registrar a certificate of the confession of Guzman, by which Aguira and others were implicated in the plot, and Martin immediately sent off this writing by an Indian messenger to Carvajal who was then at Guamanga. On the receipt of this paper, Carvajal ordered Aguira and five others to be hanged, without any further proof or examination. A short time afterwards, the registrar being sensible of the error he had committed in supplying the certificate, sent off a full copy of the confession made by Guzman, in which was an ample revocation of all he had said under torture, declaring that he had falsely charged Aguira and the others, merely to get free from torture. This was however of no avail, as it arrived too late, Aguira and the others having been already executed, although they asserted their innocence to the last moment of their lives, as was certified by the confessors who attended them at their execution; but Carvajal was inexorable.

Learning while at Guamanga, that Centeno had retired through the desert to Casabindo as he was unable to cope with Toro, Carvajal was satisfied that the affaire of the insurgent party were in a fair train in Las Charcas, where his presence was not now needed, and determined therefore to return to Lima. He was besides induced to take this step in consequence of a difference which subsisted between Toro and himself, occasioned by the charge of lieutenant general under Gonzalo having originally belonged to Toro, of which he had been deprived in favour of Carvajal. He feared therefore, lest Toro, on his victorious return from Las Charcas, being at the head of a much stronger force, might renew their former quarrel. Carvajal had likewise received letters from some inhabitants of Lima, remarking the lukewarmness of Aldana to the cause of Gonzalo Pizarro, and requesting his presence to place affairs at that city on a more secure footing. He returned therefore to Lima; but learning shortly afterwards the successful return of Centeno against De Toro, he again collected his troops and prepared to march against Centeno. With this view, he had his standards solemnly consecrated, not forgetting to impose fresh exactions on the inhabitants of Lima. On this occasion, he designated his army, The happy army of Liberty, against the Tyrant Centeno.