The spice trade linking India to Egypt, and thence Venice, had been seriously diminished and prices had shot up following the bombardment of Calicut in 1500–01 by the second Portuguese India Armada under Pedro Cabral.

Arab shipping is also being attacked directly: an Egyptian ship had been robbed and sunk by the Portuguese in 1503 as it was returning from India.

The Mamluk Sultan Qansuh al-Ghurii in 1504 first sends an envoy to the Pope, in the person of the Grand Prior of the Saint Catherine's Monastery, warning that if the Pope does not stop the exactions of the Portuguese against Muslims, he will bring ruin to the Christian Holy Place in the Levant and to the Christians living in his realm.

The Venetians, who share common interests with the Mamluks in the spice trade and desire to eliminate the Portuguese challenge if possible, send envoy Francesco Teldi, posing as a jewel buyer, as envoy to Cairo.

Teldi tries to find a level of cooperation between the two realms, encouraging the Mamluks to block Portuguese maritime movements.

The Venetians claim they cannot intervene directly, and encourage the Mamluk Sultan to take action by getting into contact with Indian princes at Cochin and Cananor to entice them not to trade with the Portuguese, and the Sultans of Calicut and Cambay to fight against them.

Some sort of alliance is thus concluded between the Venetians and the Mamluks against the Portuguese.

There will be claims, voiced during the War of the League of Cambrai, that the Venetians had supplied the Mamluks with weapons and skilled shipwrights.

The cavalry-oriented Mamluks have little inclination for naval operations, but the Portuguese keep blockading the Red Sea, and arresting Muslim merchant ships.

The sixth armada reaches Mozambique Island on June 25.

Here, Lopo Soares finds the testimonial letter left behind by Pêro de Ataíde, the former captain of the India patrol, who had died there in February.

From this missive, Lopo Soares learns of the debacle of the coastal patrol of Vicente Sodré and Calicut's attack on Cochin the previous spring.

Ataide's letter gives Lopo Soares the news of India up until February, 1504.

What Lopo Soares does not know (but probably can guess) is that at this very moment there is a desperate battle going on in Cochin.

The Zamorin of Calicut had launched a massive attack on Cochin in March, intending to capture the city and seize the Portuguese fortress.

He has brought some fifty-seven thousand troops, equipped with Turkish firearms and Venetian cannon.

The tiny Portuguese garrison at Cochin, some one hundred and fifty men under the command of Duarte Pacheco Pereira, by clever positioning, individual heroics and quite some luck, have managed to fend off attack after attack by the Zamorin's army and fleet over the past few months.

The last assault is launched in early July, after which the humiliated Zamorin calls off the invasion.

The sixth armada, crossing the Indian Ocean under the command of Lopo Soares de Albergaria, arrives at Anjadip Island, where they find two Portuguese ships repairing: those of António de Saldanha and Rui Lourenço Ravasco.

They had been part of the third squadron of the previous year's armada.

They relate their stoy of becoming lost and separated in Africa, the winter season spent harassing East African ports and Red Sea shipping, and being only able to undertake their Indian Ocean crossing this summer.

They have no idea of the whereabouts of the third ship of their squadron, that of Diogo Fernandes Pereira, having lost track of it nearly a year ago. (As it happens, Diogo Fernandes Pereira had wintered in Socotra by himself and undertaken a solo crossing to India earlier that Spring, arriving in Cochin just in time to help Duarte Pacheco fend off the assaults of the Zamorin.)

Saldanha and Lourenço accompany Lopo Soares' armada down the coast to Cannanore, where Albergaria finally hears more detailed reports from the Cannanore factor Gonçalo Gil Barbosa about the battle of Cochin.

Lopo Soares sets sail towards it at once.

The armada appears before Calicut on September 7.

Lopo Soares dispatches a message to the Zamorin, demanding he hand over any and all Portuguese prisoners to him; moreover, he demands that they also deliver the two Venetian engineers who had been helping the Zamorin build European cannon.

The Zamorin is absent from the city at the moment.

His ministers are willing to release the Portuguese prisoners, but not the Italians.

Lopo Soares subjects Calicut to forty-eight hours of continuous shore bombardment, causing great damage, then proceeds south to Cochin.

Lopo Soares had left Mozambique on August 1.

Although instructed by his regimento to make a stop in Malindi, it is possible he sails for India directly from Mozambique.

Damião de Góis reports the sixth armada did stop at Malindi, and was (as usual) well received by the Sultan of Malindi.

Góis asserts the Sultan of Malindi not only resupplied the ships, but provided Lopo Soares with a Muslim pilot named 'Debucar'.

He also handed over sixteen Portuguese shipwrecked sailors, survivors of Ataíde's capsized ship, who had been collected by Malindi boats earlier that year.

The sixth armada remains in Malindi only two days, before setting off on their Indian Ocean crossing.

Cochin’s Trimumpara Raja and the tired Portuguese garrison meet the armada at Fort Manuel, whose commander Duarte Pacheco Pereira had recently left to check on the Portuguese factory at Quilon.

Greetings and gifts exchanged include a sizable sum of cash sent by Manuel I of Portugal as a reward for the Trimumpara Raja's alliance.

With the Cochin spice markets starved by the recent siege, Lopo Soares sets about collecting spices from elsewhere.

Four or five ships are sent down to Quilon to load up.

Two ships are sent out to patrol the coast south of Calicut, and seize whatever merchant ships they can—and take their spice cargoes—while another, joined by five local bateis (pinnaces), are dispatched on patrol duty inside the lagoon.

Hearing of the armada's arrival, Duarte Pacheco sets sail back to Cochin and meets Lopo Soares on September 14 (October 22 according to Castanheda).

Lopo Soares receives reports while in Cochin that the Zamorin of Calicut has dispatched a force to fortify Cranganore, the port city at the northern end of the Vembanad lagoon, and the usual entry point for the Zamorin's army and fleet into the Malabari backwaters.

Reading this as a preparation for a renewed attack on Cochin after his armada leaves, Lopo Soares decides on a preemptive strike.

He orders a squadron of around ten fighting ships and numerous Cochinese bateis and paraus, to head up there.

The heavier ships, unable to make their way into the shallow channels, anchor at Palliport (Pallipuram, on the outer edge of Vypin island, guarding the channel between Cranganore and the sea).

Converging on Cranganore, the Portuguese-Cochinese Vembanad fleet quickly disperses the Zamorin's forces on the beach with cannon fire, and then lands an amphibian assault force of some thousand Portuguese and another thousand Cochinese Nairs, who take on the rest of the Zamorin's forces in close combat.

The Zamorin's forces are defeated and driven away from the city.

The assault troops capture Cranganore, and subject the ancient city, the once-great capital of the Chera Dynasty of Kerala, to a thorough and violent sacking and razing.

Even while the main fighting is still going on, deliberate fires are set around the city by squads led by Duarte Pacheco Pereira and factor Diogo Fernandes Correa.

The fires quickly consume most of the city, save for the Syrian Christian quarters, which are carefully spared (Hindu and Jewish homes are not given the same consideration).

Hearing of the attack, the Zamorin dispatches a hastily-formed Calicut fleet, some five ships and eighty paraus, to save the city, but the idling Portuguese ships near Palliport intercept and defeat them in a brief naval encounter.

Two days later, the Portuguese receive an urgent message from the ruler of Tanur (Tanore), whose kingdom lies to the north, on the road between Calicut and Cranganore.

The raja of Tanur had come to loggerheads with his overlord, the Zamorin, and offered to place himself under Portuguese suzerainty instead, in return for military assistance.

He reports that a Calicut column, led by the Zamorin himself, had been assembled in a hurry to try to save Cranganore, but that he managed to block their passage at Tanur.

Lopo Soares immediately dispatches Pêro Rafael with a caravel and a sizeble Portuguese armed force to assist the Tanurese.

The Zamorin's column is defeated and dispersed soon after its arrival.

The raid on Cranganore and the defection of Tanur are serious setbacks to the Zamorin, effectively placing the Vembanad lagoon out of the Zamorin's reach.

Any hopes the Zamorin had of quickly resuming his attempts to capture Cochin via the backwaters are effectively dashed.

The Battle of Cochin has broken his authority.

Lopo Soares, his naus loaded with spices from the markets of Cochin and Quilon (and topped off with cargoes from seized merchant ships), prepares his departure from Cochin.

Duarte Pacheco Pereira, the hero of the battle of Cochin, is slated to be relieved as captain of Fort Manuel.

It is said that the Trimumpara Raja of Cochin, who had become personally attached to Duarte Pacheco during the battle earlier that year, was beside himself with grief and did everything he could to persuade Lopo Soares to let Duarte Pacheco stay on, but Lopo Soares had refused.

Bowing to inevitability, the Trimumpara had offered Duarte Pacheco a free cargo of pepper as a personal reward for his services, but Duarte Pacheco, knowing how the Trimumpara Raja had been personally impoverished by the war, had refused to take it.

Duarte Pacheco's replacement as capitão-mor of Fort Manuel of Cochin is nobleman Manuel Telles de Vasconcelos (or Manuel Telles Barreto, according to Barros).

Lopo Soares leaves Manuel Telles with three (possibly four) ships: one nau, and two caravels, under the commands of Diogo Pires and Pêro Rafael (and possibly Cristovão Jusarte (Lisuarte Pereira?

)), all veterans of the battle of Cochin.

Lopo Soares annexes what remains of the earlier fleets (e.g., Diogo Fernandes Pereira, Antonio de Saldanha, etc.)

into the returning armada.

Overall, Lopo Soares is bringing back to Lisbon two more ships than he left with.