The Ráni of Quilon, an important pepper port, sent a message requesting that the Portuguese would come to her port also to obtain goods. But Dom Vasco da Gama feared to offend the Rájá of Cochin by trading elsewhere, and it was only after receiving the express consent of the latter monarch that he took two shiploads of pepper from Quilon. Having taken on board a lucrative cargo Dom Vasco da Gama returned once more to Portugal, leaving behind him the squadron designed for that purpose under the command of one of his relations, Vicente Sodré.
The Admiral also made a treaty with the Rájá of Cannanore, a ruler nearly as powerful as the Rájá of Cochin, which provided that the former should never make war on the Rájá of Cochin, and should refuse to assist the Zamorin in case that powerful ruler undertook such an attack, and he also established a factory at Cannanore. Vicente Sodré cruised for some time on the Malabar coast, as he had been directed to do, and then sailed for the coast of Arabia in order to intercept the ships of Muhammadan merchants trading between India and Egypt. He had, however, but small success; for in the summer of 1503 his squadron was wrecked on the Abd-el-Khuri rocks off Socotra, three of his ships were lost, and Sodré himself was drowned.
In 1503 three separate squadrons were despatched to the East from Portugal under the command respectively of Affonso de Albuquerque, the future Governor, Francisco de Albuquerque, his cousin, and Antonio de Saldanha, the last of whom was ordered to explore the African coast and gave his name to Saldanha Bay. Francisco de Albuquerque, who arrived first in India, was only just in time to succour the Rájá of Cochin. The Zamorin of Calicut, as Vasco da Gama had foreseen, had attacked the Rájá of Cochin in force, at the instigation of the Moplas, as soon as Sodré's squadron had left the Malabar coast. The situation of the Cochin Rájá was one of peril. He had been driven from his capital and was being besieged in the island of Vypín, and he welcomed the arrival of the ships of Francisco de Albuquerque with cries of joy.
The Portuguese met with little difficulty in defeating the army of the Zamorin and in restoring their ally, the Rájá of Cochin, to his dominions. But the extremity of the danger had been such that the two Albuquerques built a strong fort of wood and mud, mounted with artillery, at Cochin; and when they departed they left behind them not only a squadron of war-ships, as Vasco da Gama had done in the previous year, but also a garrison of trained soldiers for the new fort, both under the command of Duarte Pacheco. The two cousins Albuquerque had more than one difference of opinion, and Affonso, after sailing to Quilon, where he made a treaty with the Ráni and established a factory, returned to Portugal with his squadron, without waiting for Francisco.
No more valiant warrior illustrated the glory of the Portuguese name than Pacheco. The Zamorin of Calicut, as soon as the Albuquerques had left the coast, advanced against Cochin with a more powerful army than he had set on foot in the previous year. Pacheco had only 150 Portuguese soldiers, but nevertheless he inspired perfect confidence into the mind of his ally, the Cochin Rájá. That king, at the request of the Portuguese commander, abandoned his first idea of deserting his capital, and placed all his resources at the disposition of Pacheco, who repulsed every assault which the Zamorin made upon Cochin, and defeated his troops in four pitched battles beneath the walls of the city. The valour of the Portuguese greatly impressed the Zamorin, who witnessed the last of these battles, and the Hindu ruler soon repented his compliance with the demands of the Mopla merchants.
After defeating the Calicut troops on land Pacheco took the personal command of his squadron at sea, and defeated the Calicut fleet of fifty-two ships. The news of these battles spread abroad through India. Many Rájás in the interior sent envoys to the Portuguese commander, and the Zamorin himself earnestly sued for peace. The prestige of the Portuguese was assured by Pacheco's victories, and from this time forth for nearly a century the inhabitants of Southern India recognised that the Portuguese were stronger than themselves, and were eager to trade with them or to make alliances.
Pacheco increased his reputation by a daring march to Quilon, where he rescued the Portuguese factor from much danger; for at Quilon, as at all the ports along the coast, the Moplas showed an unrelenting hatred to the European agents. When Lopo Soares de Albergaria, son of the Chancellor of Portugal, who commanded the squadron sent from Portugal in 1504, reached the Malabar coast he found the Indian ports ringing with news of Pacheco's victories. He once more bombarded Calicut, and then returned to Portugal, bringing with him a rich cargo and also the gallant Portuguese commander. It is a lasting disgrace to King Emmanuel that he neglected to reward the hero of Cochin according to his merits. He gave his faithful servant a distinguished reception, and had sermons preached in his honour in every church of Portugal, but eventually, like Camoens and other famous Portuguese warriors, Pacheco was left to die in poverty and misery.
It was after the return of Pacheco, and probably owing to that brave man's advice, that King Emmanuel in 1505 inaugurated a new departure in the relations between Portugal and the East. Pacheco's victories made it evident that it was not only possible for Portuguese garrisons and local squadrons to defend the Portuguese factors, but that they could defeat and conquer powerful native monarchs. A conception of the ease by which a Portuguese empire could be established in the East was now grasped by King Emmanuel. His ideas were still mainly commercial, but he began to perceive also that the safe maintenance of trade and commerce would necessarily involve a regular war to the death with the Muhammadan powers who had reaped the greatest profit from the trade of the East with Europe. Hitherto the Portuguese in India had striven with the Muhammadan Moplas settled on the Malabar coast; but it now became apparent that the Muhammadans of Egypt, Persia, and Arabia would come to the help of their co-religionists. Emmanuel decided therefore to maintain a more powerful army and navy in Asia than he had yet despatched to the Eastern seas, and to replace annual expeditions by a local establishment.
Such a force had to be commanded by an experienced general, who should also be a man of rank, in order to exercise undisputed sway over the whole resources of Portugal in the East. For this important office the king first selected Tristão da Cunha, a daring and skilful commander and navigator. But Tristão da Cunha was struck with temporary blindness, and King Emmanuel then chose Dom Francisco de Almeida, a member of one of the most illustrious families of Portugal. Almeida when he sailed received only the title of Chief Captain, but on his arrival at Cannanore on September 12, 1505, he took the high-sounding title of Viceroy of Cochin, Cannanore, and Quilon.
The great Portuguese nobleman looked upon the situation of affairs in a different light to his predecessors. He was not satisfied with the idea of protecting the Portuguese trade which had been established, but considered it his duty to destroy the Muhammadan traders and to secure for his countrymen the entire command of the Eastern seas. Since it was necessary for the Portuguese fleets to have some safe ports at which they could refit before and after crossing the Indian Ocean, he built a strong fortress at Quiloa (Kilwa), about 200 miles south of Zanzibar, and made the Chief of Mombassa between Zanzibar and Melinda tributary. He also organised, for the first time, a regular Portuguese Indian pilot service, for he felt it to be a weakness to the Portuguese to be dependent on native pilots like the men who had shown Vasco da Gama the way across the Indian Ocean.