When the King of Tidore heard of their piracies, and of the number of Malay seamen they had captured, he dealt with the question humanely and diplomatically, suggesting that all these prisoners should be returned by him to their island homes, where they could make known the greatness and splendour of the kingdom of Spain. This the Spaniards consented to do, reserving only the people from Brunei, who, as already related, were brought to Seville. As the king was a very zealous Muhammadan, they also killed all the swine on board to please him, and he in return gave them a large number of goats and fowls, besides quantities of vegetable food, including sago derived from the sago palm, which was the principal nourishment of these Molucca Malays.

In the Island of Ternate there arrived presently a Portuguese in a Malay prau, who gave them very interesting information derived from the visit a year previously of a Portuguese ship. The survivors of Magellan's expedition learnt then that the main facts of their voyage had become known to the King of Portugal some time after their departure, and that ships had been sent to the Cape of Good Hope and to other places to prevent their passage. When it was learnt that they had rounded South America and made their way across the Pacific, an attempt was made to dispatch a Portuguese fleet of six ships to the Molucca Islands to capture Magellan's expedition. But this fleet was prevented from accomplishing its purpose through its being detained in the Red Sea by the necessity of fighting a Turkish fleet.

Whilst the two ships stayed at Tidore many festivities took place in connection with the visits of chiefs or kings of the other Molucca Islands. These Malay princes came in their praus, some of which had three tiers of rowers on each side, in all 120 rowers, and they hoisted great banners made of white, yellow, and red parrot feathers. Gongs of bronze and brass were sounded and timed to the rowers' actions. Sometimes the praus would be filled with young girls, female slaves (though not feeling any of the misery of slavery), who were to be presented as household servants to the daughters of chiefs betrothed to this and that heir apparent. The kings of the islands sat on rich carpets, no doubt received by indirect trade from Persia. They wore cloths of gold and silk manufactured in China, and the women were clad in beautiful silk garments from the waist to the knees. They brought with them, amongst other presents for the King of Spain, "two extremely beautiful dead birds". These were as large as thrushes, with a small head and a long beak. They were of a tawny colour, but with beautiful long plumes of a different tint.[39] The natives who brought them called them the Birds of God, and said that they came from the terrestrial Paradise. This was probably the first mention in our European literature of Birds of Paradise.

At last the ships were ready to go, in December, 1521. Juan del Cano (or de Elcano, as it is sometimes written), an officer hitherto scarcely mentioned, had been elected captain of the Victoria, and the command of the Trinidad had been given to Espinosa, replacing Carvalho, the pilot, who had behaved very badly in regard to the captured natives as well as towards the members of the expedition. [It was Carvalho who refused to stay and ransom poor Juan Serrano.] The Victoria set sail on her way towards Timor and the Indian Ocean, when her cruise was suddenly stopped by the news that her consort the Trinidad had suddenly developed a dangerous leak. They found the water rushing in as through a pipe, and pumping was useless. The kindly King of Tidore sent down divers, who remained more than half an hour under water, endeavouring to find the leak. Some of these even remained an hour under water (this no doubt was a great exaggeration), and, by wearing their long hair loose, attempted to find the leak by letting it be drawn by the suction of the water towards the place. But it was decided at last that the Victoria should start for Spain and the Trinidad remain behind for repairs.[40] The Victoria therefore left with a crew of forty-seven Europeans and thirteen Malays, chiefly from Borneo.

The Victoria on her way to Timor passed the Shulla Islands (Xulla), and heard from their Malay pilots that the inhabitants were naked cannibals. In other islands there were pigmies (negritos); others, again, were more civilized, producing rice, pigs, goats, fowls, sugar cane, and a delicious food made of bananas, almonds, and honey, wrapped in leaves and smoke-dried, then cut into long pieces. Buru Island was noted (though they did not land there) as inhabited by Muhammadan Malays on the coast and cannibal savages in the interior; also the Banda Islands, producing mace and nutmeg. After leaving the vicinity of Buru the Victoria encountered a fierce storm, which drove them to seek refuge in a harbour of a lofty island[41] which was inhabited by savage, bestial people, eating human flesh and going naked, except that their warriors wore armour made of buffalo hide and goatskins. They dressed their hair (like the New Zealanders) high up on the head, held in position by long reed pins, which they passed from one side to the other. Their beards were wrapped in leaves and thrust into small bamboo tubes. They were the ugliest people Pigafetta had seen, and were armed with bows and arrows of bamboo. Nevertheless they behaved in a friendly way to these Spaniards and sold them quantities of provisions, beeswax, and pepper.

On 26 January, 1522, the Victoria reached the Island of Timor, where it laid in a great supply of buffaloes, pigs, and goats. The people, though going almost naked, wore many gold and brass armlets and ear-rings, and bamboo combs in their hair adorned with gold rings.

On 11 February, 1522, the Victoria sailed away from Timor into the great Indian Ocean. She was only a little vessel of 85 tons, and she had to buffet her way amidst various storms and high waves across the southern Indian Ocean, as far as the forty-second degree of south latitude before she could beat up north and round the Cape of Good Hope. The sufferings on board were terrible, the ship leaked badly and the pumps were always going, the provision of buffalo meat had putrefied, as they had had no salt to preserve it. There was little other food than rice. After rounding the Cape of Good Hope it took them a further two months before they could land anywhere to obtain fresh provisions, and twenty-one men died of scurvy and starvation during this terrible period. At last, constrained by their despairing condition, they stopped off the Island of Sant Iago, in the Cape Verde archipelago, which for some time had been a settlement of the Portuguese. Here they sent a boat ashore for food, with a concocted story to deceive the Portuguese into believing that the Victoria was a ship coming from Spanish America and driven out of her course by storms. But on its second voyage to the shore the boat, containing thirteen men, was detained, because, having no money, they offered cloves in payment of the things they purchased. Seeing from a distance that the men had been arrested, the captain of the Victoria felt obliged to abandon them to their fate and hastily sailed away.

At last, on 8 September, 1522, the Victoria, having sailed into Spain up the Guadalquivir River, dropped anchor at the quay of Seville and discharged all her artillery in crazy joy at this return to the Motherland. On the following day all the survivors of this wonderful expedition—eighteen in number—went in shirts and barefooted, each man holding a candle, to visit the shrines of Santa Maria de la Victoria and of St. Mary of Antiquity in two different churches. As to the thirteen men left behind, they were not so ill treated after all by the Portuguese, but were ultimately dispatched to Seville, so that it may be said of the five ships which started with Magellan in 1519 to reach the Moluccas by way of the Pacific Ocean only one returned to Spain—the Victoria, the Trinidad having been lost near the Spice Islands; while of the original 265 men (more or less) who left Spain in 1519 only 36 returned to Spain after circumnavigating the globe—18 in the Victoria, 13 in Portuguese ships from the Cape Verde Islands, and 5 survivors from the Trinidad sent back by the Portuguese from Malaysia.

In spite of all these disasters, however, the cargo of cloves and spices brought back by the Victoria sufficed, not only to pay the whole cost of the equipment of the original expedition of five ships, but left a profit of about £200 in value over and above.