Shortly after its conquest, Albuquerque set sail to conquer Malacca in Malaysia, leaving Lopes behind as part of the garrison, with orders to keep the peace and rule over the local population.
When Albuquerque returned nearly two years later, he found Goa under siege and some of the men had defected to the enemy side, and some, including Lopes himself, had married native women and converted to Islam.
He was bound with ropes to two wooden posts, and Albuquerque's men severed his nose, ears, right arm, and left thumb (according to others, his index and middle fingers as well) in a public square.
The interior of Saint Helena was a thick old-growth forest of ancient gumwood trees and other native plants that had colonized the island as many as 10 million years ago.
The following is from a contemporary account of the first ship to encounter Lopes after he had been left on Saint Helena, found in a Hakluyt Society journal: The crew was amazed when they saw the grotto and the straw bed on which he slept...and when they saw the clothing they agreed it must be a Portuguese man.
So they took in their water and did not meddle with anything, but left biscuits and cheeses and things to eat and a letter telling him not to hide himself the next time a ship came to the island for no one would harm him.
After 10 years on the island, Lopes agreed to return to Portugal to see his family, visited King João III and then traveled to Rome, where Pope Clement VII absolved him of the sin of apostasy.