The brothers of Pizarro, who was at Lima, had much difficulty to maintain possession of the capital; all communication between them and the governor being cut off, and the place was vigorously besieged by Manco Capac and his brothers Paullu and Villaoma, for eight months, during which time the Spaniards lost many men. Almagro hearing of these disasters, thought this a convenient time to assert his old pretensions to the government of Cuzco, and accordingly marched from the frontiers of Chili to that place in 1537. He was met by the Inca, who under pretence of making overtures to him, drew him into a snare, from which he narrowly escaped, with the loss of several of his men.
The brothers of Pizarro finding they had now a new enemy to withstand, prepared Cuzco to undergo a formidable siege; but having lost six hundred men during the attacks of the Peruvians, they were surprised by the troops of Almagro who forced them to submit, and declared himself governor of the place, imprisoning Fernando and Gonzalo Pizarro, and quartering Philipillo, who was taken prisoner in the ambush of the Inca.
Manco Capac finding that Almagro was too strong to be easily ejected, retired to the mountains, but his brother Paullu remaining at Cuzco, was raised to the throne of Peru by Almagro. It was some time before all these untoward tidings reached the ears of the new Marquess Pizarro; he first heard of the attack of the city by the Inca, and imagining it to be a trivial affair, detached small parties at different periods to the assistance of his brothers; none of these reached their destination, being always cut off by the Peruvians in the narrow and difficult passes of the mountains. Some few of these people escaping from the massacre, which always took place on their being surprised, returned to Lima, and related the fate of their companions to the Marquess, who recalling all his outposts, nominated Alvarado to the command of the army, and sent him towards Cuzco, with 500 men; but being closely invested at Lima by the Peruvians, under Titu Yupanqui, a brother of Manco Capac, he sent off all his vessels to Panama, fearful that the troops might otherwise desert, and by these ships he implored assistance from the governors of New Spain and the West Indies.
Alvarado, after a harassing march, and fighting severe battles with the Peruvians, halted near the bridge of Abancay on the Apurimac; at which place he was met by a messenger from Almagro, insisting on his acknowledging the title he bore to the government of Cuzco. An unsatisfactory reply being sent, Almagro advanced to attack the army under Alvarado, and by dint of bribery, corrupting the greater part of it, obtained a bloodless victory on the 12th of July, 1537.
Pizarro hearing nothing of his general, and receiving a strong reinforcement from Hispaniola, marched from Lima with 700 men to relieve his brothers at Cuzco from the Peruvians, not having yet heard of the usurpation of Almagro. Having marched twenty-five leagues, he received the intelligence of the death of one of his brothers, the imprisonment of the other two, and of the determined opposition of Almagro; this news so much alarmed him that he immediately returned to Lima, and dispatched a messenger to Cuzco to treat with Almagro; but that officer instead of returning an answer marched to within twenty leagues of Lima, where he was met by Pizarro who seemed earnest to heal the breach amicably; but after various endeavours to obtain this end, he found it necessary to have recourse to force; and Almagro, finding himself unable to cope with him, retreated to Cuzco, whither Ferdinand Pizarro pursued him: a dreadful battle then took place near that city, on a plain called Salinas or Cachipampa, in which Almagro was defeated and taken prisoner, and was soon afterwards brought to trial and beheaded.
This important affair being settled, the marquess dispatched troops in all directions to conquer and subdue those provinces which remained under the domination of the Indians. In these expeditions, and in settling the affairs of his government, Pizarro was fully occupied for two years, during which time he was much distressed by the mutinous conduct of the Almagrian party, who at last assassinated him on the 26th of June, 1541.
Soon after the untimely death of Pizarro, Vaca de Castro was appointed governor, while the court of Madrid were employed in taking measures to put a stop to the contentions of the colonies. He was removed to make room for Blasco Vela, who was nominated the first viceroy of Peru, and who landed at Tumbez in the month of February, 1543. The conduct of this viceroy increased the disaffection and contention of the colonists, many of whom siding with Gonzalo Pizarro, chose him as their leader. After various actions with the royal troops, Gonzalo at last utterly defeated them in a pitched battle, in which the viceroy was slain.
Upon this occasion Gonzalo Pizarro was advised to assume the sceptre of Peru, but he chose to treat with Spain. During the interval which elapsed before the return of his ambassadors, Pedro de la Gasca, a priest, was sent over as president: finding he could not persuade Pizarro to any terms, he gave him battle, in which the latter was taken, and being brought to trial by the president, was beheaded on the 10th of April, 1548.
After this action, Gasca set himself about to reform abuses, and render the government more stable; he was occupied in this work till 1550, when wishing to return to a private station, he quitted Peru, and entrusted the command of the presidency to the royal court of audience, till the pleasure of the king should be manifested.
After the departure of Gasca, till the arrival of the second viceroy, Mendoza, Peru continued to be in a state of continual ferment, which lasted more or less until his death. The next viceroy was the Marquess de Canete, who arrived in Lima in July 1557. He was succeeded in July 1560, by the Conde de Neiva, who, dying suddenly, was replaced by Lope Garcia de Castro with the title of president, until Francisco de Toledo arrived from Spain, to assume the viceregal government, who had been only two years in Peru, when he attacked Tupac Amaru, the son of Manco Capac, who had taken refuge in the mountains. A force of two hundred and fifty men was detached to Vilcapampa under Martin Garcia Loyola, to whom the Inca surrendered himself, with his wife, two sons, and a daughter, who were all carried prisoners to Cuzco.