Standing atop the rugged, barren peak of Al Hallaniyah Island, eyeing the blue-grey Arabian Sea as it lashed the rocky coast below, David Mearns tried to transport himself back 500 years.

The sky was dark with storm clouds, the sea a raging, surging maelstrom. Two ships, heedlessly anchored on the exposed northern side of the island, were whipped about by the winds and waves, stretching their moorings to the breaking point. Once adrift, the wooden vessels were driven shorewards and bashed against the rocks. One got close enough to the beach for its crew to escape before it broke apart completely. The other splintered and sank in deep water, dragging everyone on board, including its captain, to the bottom of the sea.

Mearns had spent half a year reading accounts of that disaster, which doomed part of a fleet led by the legendary Portuguese explorer Vasco da Gama. He’d internalised everything he could find about the weather, the vessels, the island, the perils of the Arabian Sea during the “Golden Age of Exploration” half a milennium ago. And he knew that at least one unparalleled example of a ship from that time lay somewhere within his reach. If only he could find it.

“Our team stood at the top of the island and watched the waves come in, and put themselves in the place of the Portuguese, where they would have anchored and where the storm would have dashed them along the coastline,” Mearns told National Geographic. But the initial search didn’t take much more time than the visualisation: “Then they snorkelled around and in 20 minutes started seeing cannonballs that were obviously from a European ship.”

That was in 1998. It would be another decade and a half before Mearns’s shipwreck salvage company, Blue Water Recoveries, returned to conduct a full excavation of the site in partnership with the Ministry of Heritage and Culture in Oman. Pushed around by high-energy wave surges the divers called “the washing machine”, the ship and its riches had been buried deep in sand at the bottom of the sea.

But in the end, Mearns announced on Tuesday at a press conference in Muscat, the archaeologists did find what they were looking for. The wreck uncovered off the coast of Al Hallaniyah is almost certainly Da Gama’s ship Esmeralda, which sank with its captain and Da Gama’s uncle, the swashbuckling, rapacious Vincente Sodré, on board in 1503.

A report on the find published in the journal Nautical Archaeology is still considered “interim” — thousands of artefacts dug up from the wreck site have yet to be analysed. But, if Mearns’s conclusion is borne out, the Esmeralda will be the oldest ship from the Age of Exploration ever to be excavated.

“It is fascinating to work on a site that is involved in such early European maritime connections with the Indies,” Dave Parham, a professor at Bournemouth University and the archaeological director of the expedition, said in a press release. “The armaments that the site has produced are already providing us with information about the martial nature of these voyages and the site has the potential to tell us much more about the men and ships that undertook these adventures and the peoples that they encountered.”

Among those armaments are a bronze ship’s bell dated 1498 — the earliest ship’s bell to be discovered, a copper alloy disc bearing the Portuguese royal coat of arms and thought to be part of an astrolabe and, rarest of all, a tiny silver medallion known as “the ghost coin of Dom Manuel I”.

The coin, minted by Portuguese King Dom Manuel in 1499, was an “indio”, specially made for trade with India. It’s a “ghost” because, until now, only one has ever been found.

The discovery of the second ghost coin hints at what the ill-fated Esmeralda was doing in the Arabian Sea in the first place.

She’d been part of a massive armada led by Da Gama in order to conduct trade — and in many cases, wage war — in India. The fleet followed the route famously pioneered by Da Gama four years earlier: a circuitous, 24,000-mile voyage around the Cape of Good Hope and up Africa’s eastern coast that took the better part of a year and killed the better part of Da Gama’s crew. Nevertheless, his journey to India provided the first link between Europe and the spices of the East that didn’t depend on overland routes controlled by Arab traders and Venetian merchants. To 15th century Portugal, eager for trade riches and finally some flavour in their food, Da Gama’s new route was a very big deal.

That first successful voyage was a turning point in world history: the beginning of the ages of exploration, imperialism and globalisation, with all their change and brutality. And what happened on Da Gama’s second voyage, including the demise of the Esmeralda, was a grim harbinger of the violent centuries that lay ahead — for both the colonised and the colonisers.

The armada set out in 1502, the fourth such fleet to be sent by King Dom Manuel. Its predecessors hadn’t fared well — the people of Calicut (now Kozhikode, on India’s western coast) didn’t take kindly to being bossed around by entitled Europeans, and the Portugese had responded by bombarding the city to shreds.

So Da Gama’s fleet was well-stocked with weaponry and given broad licence to use it. He tried (not entirely successfully) to subdue uncooperative Indian kingdoms and attacked any other ship he encountered in the Indian Ocean, including one carrying Muslim pilgrims on their way back from Mecca. Da Gama burned the boat along with its 300 passengers, according to an eyewitness, sparing only 17 children — who were then baptised without their consent.

When he headed back to Portugal in early 1503, Da Gama left behind a squadron of five ships led by his two uncles — Vincente and Bras Sodré — to keep doing more of the same. The goal, according to the Nautical Archaeology report, was “to forcibly control and dominate the spice trade”.

The Sodré brothers had their own ideas, though. Rather than patrol the Indian coast, they set out for the Gulf of Aden, which was full of lucrative opportunities for piracy on the high seas. They spent the next several months capturing Arab ships, plundering their cargo and killing their crews. According to an account from one of the other commanders, the Sodres’ decision rankled the rest of the squadron — not so much because of the violence it involved, but because crew members wanted a cut of the loot.

By April, monsoon season had arrived, and one of the ships was in need of repairs, so the squadron retired to Al Hallaniyah for some rest and trade. The local fishermen warned the Portuguese that their choice of port — on the exposed windward side of the island — was a poor one, but the Europeans were recklessly confident in the strength of their iron anchors and hulking ships. They moved the squadron’s smaller ships to the other side of the island, away from the fiercest winds, but left Vincente Sodré’s Esmeralda and Bras’s Sao Pedro where they were.

Their haughtiness proved deadly: when the storm came, both vessels were dashed against the rocky shore. Vincente went down with his ship, and Bras died not long after of undetermined causes.

Five hundred years later, it seems that the ship that bore Vincente’s ambitions and loot has finally been found. But the Sodré brothers — and the 100 or so crew members who died with them — are still missing.

According to National Geographic, a survey of Al Hallaniyah Island revealed dozens of burial cairns that are thought to be non-Islamic (they’re oriented differently from burial sites for Muslims). But when the sites were excavated, researchers couldn’t find any human remains. It’s likely that the buried bodies deteriorated from prolonged exposure to animals and the elements.

It was those missing men that Mearns thought about during his long search for the Esmeralda.

“A shipwreck site is not a pretty thing,” he told National Geographic. “It’s the scene of a tragedy … it’s a place you have to treat with respect because many people died there.”

—By arrangement with The Washington Post

Published in Dawn, March 18th, 2016