As the marquis was now reinforced by a considerable number of troops, he thought himself in condition to send assistance to those parts which were in greatest danger, and detached therefore Alfonso Alvarado with three hundred horse and foot, who pillaged several districts with very little resistance from the Indians. But about four leagues from the city of Pachacamac, he was violently attacked by the Indians, whom he defeated with considerable slaughter; after which he continued his march towards Cuzco. On this march the army of Alvarado suffered great hardships in passing across a large extent of desert country, five hundred Indians who attended as servants perishing of thirst; and it is said that all the Spanish infantry must have died of thirst and fatigue, if they had not been relieved by the activity of the cavalry in bringing them water from a distance. After reaching the province of Jauja, Alvarado was joined by Gomez de Tordoya with two hundred horse and foot, who had been sent after him. His force being augmented to five hundred men by this reinforcement, Alvarado proceeded to the bridge of Lumichaca, where he was surrounded by a numerous army of hostile Indians. Having defeated these in battle, he continued his march to the bridge of Abancay191, continually harassed by the Indians. At that place he learned that Ferdinand and Gonzalo Pizarro had been imprisoned by Almagro, who had taken possession of Cuzco; on which he resolved to halt where he then was till he might receive precise orders from the marquis for his farther proceedings.

When Almagro was informed of the arrival of Alfonso Alvarado at Abancay, he sent Diego Alvarado to wait upon him, attended by seven or eight horsemen, with orders to notify his commission as governor in these parts. Alfonso, after examining the commission, declared that he did not consider himself competent to decide upon an affair of such high importance, and that the documents ought to be communicated to the marquis. Almagro had come part of the way from Cuzco towards the camp of Alvarado, where he waited the return of his messenger; and not seeing him at the time he expected, he became afraid that Alvarado had detained him and might advance to Cuzco by another road. He returned therefore to Cuzco in all haste to provide for his defence. Learning the discontent of Lerma, on account of having been superseded in the command of the army by the marquis, and that he was disposed to come over to his side with eighty men, Almagro marched out from Cuzco with his troops a fortnight afterwards, and advanced towards the army of Alfonso Alvarado. While on the march, the advanced guard belonging to Almagro, by means of an ambush, made Pedro Alvarez Holguin prisoner, who had been sent out on discovery by Alvarado. On learning this circumstance, Alvarado meant to have arrested Pedro de Lerma, as he entertained suspicions that he was in correspondence with Almagro; but Lerma had previously escaped to the enemy, carrying along with him the signatures of all those who had joined him in the plot for deserting to Almagro.

After the junction of Lerma, Almagro approached during the night to the bridge of Abancay with one part of his army, where he knew that Gomez de Tordoya and a son of Colonel Vilalva waited for him; and he detached at the same time a large body of his troops to a ford of the river, where those who had conspired in his favour along with Lerma had the guard. By these men the troops of Almagro were received as friends, so that they passed the river without opposition. Some of these conspirators contrived during the night to throw above fifty lances belonging to the cavalry of Alvarado into the river. Owing to all these circumstances, when Alvarado proposed next morning to have attacked the enemy, he found himself abandoned by the conspirators; and a considerable number of his own troops, not being able to find their arms, did not come up in time for the attack. By these means Almagro got an easy and bloodless victory, not a single Spaniard being killed on either side, Rodrigo Orgognez only losing several of his teeth by a stone thrown from a sling192. After the capture of Alfonso Alvarado, the Almagrians pillaged his camp, and carried all the adherents of Pizarro as prisoners to Cuzco, where they were harshly treated. In consequence of this victory the partizans of Almagro were so much elated, that they used to say the Pizarros might now retire from Peru to govern the Mangroves under the equator.

In consequence of the victories which Alvarado had gained over the Indians at Pachacamac and Lumichaca, as already mentioned, the Inca and Titu Yupanqui were obliged to retire from before Lima, which they had in a manner blockaded. By this circumstance the marquis found himself at liberty to act in support of his interest at Cuzco; and having received considerable reinforcements from various parts, he began his march for Cuzco at the head of more than seven hundred men, horse and foot. In this expedition, his only purpose was to succour his brothers against the Peruvians, as he had not hitherto received information of the return of Almagro from Chili, or any of those other events which had taken place, as before related. Most of the troops by which the marquis was lately joined, were sent by Don Alonso de Fuenmayor, archbishop and president of Hispaniola, under the command of his brother Don Diego de Fuenmayor. Besides these, Gaspar de Espinosa had brought some troops from Panama, and Diego de Avala had brought others from Nicaragua. With this army the marquis set out from Lima for Cuzco, taking the way of the plain, and arrived in the province of Nasca, about twenty-five leagues from Lima193. At this place he received intelligence of the return of Almagro, the death of one of his brothers and imprisonment of the other two, the defection of Lerma, and the capture of Alvarado. He was sensibly affected by this afflicting news; and considering that his troops were only prepared for contending against Indians, he thought proper to return immediately to Lima to take proper measures under the present emergency of his affairs.

Soon after his return to Lima, the marquis sent the licentiate Espinosa to endeavour to bring about an accommodation with Almagro. Espinosa was directed to represent to Almagro, that if his majesty were informed of the disputes between them, and the evil consequences of these upon the condition of the colony, he would assuredly recal both, and send some other person to assume the government of Peru, who would reap the rich fruit of their joint labours. If Almagro refused to listen to these remonstrances, and to enter into a friendly accommodation, Espinosa was instructed to request that he would set the brothers of Pizarro at liberty, and would remain at Cuzco without attempting any farther hostilities, untill they had laid a statement of their differences before his majesty, and had received his final orders respecting the boundaries between their governments. Espinosa was unable to persuade Almagro to agree to any accommodation, and soon afterwards died. Leaving Gabriel de Roias as his lieutenant in Cuzco, with the charge of Gonzalo Pizarro and Alonso de Alvarado, Almagro descended into the plain with a considerable force, carrying Ferdinand Pizarro along with him. He penetrated into the province of Chancay, which is only twenty leagues from Lima, where he even established a colony or garrison, in a place which was without any manner of doubt within the province of the marquis.

On the return of the marquis to Lima, he made additional levies of troops; giving out openly that he was reduced to take up arms against Almagro, who had invaded his government. In a few days he assembled an army of seven hundred men, among whom was a considerable body of musqueteers, which had been brought from Flanders with the necessary arms and ammunition by Pedro de Vergera, along with the troops of Diego de Fuenmayor. Hitherto there had not been a sufficient number of musquets in Peru to form entire companies of that species of troops; but on the present occasion the marquis was enabled to arm two companies with that powerful weapon, one of which was commanded by the before named Pedro de Vergera, who had been formerly sent to discover the province of Bracamoras. Nugno de Castro was appointed captain of the other company of musqueteers. Diego de Urbina, nephew of the maestre de campo Juan de Urhina, was made captain of the pikemen. Diego de Roias, Peranzures, and Alfonso de Mercadillo, were appointed captains of horse: Pedro de Valdivia maestre de campo, and Antonio de Vilalva sergeant-major, who was son of Colonel Vilalva.