The expedition claimed the lives of all 129 men and has gripped the public’s imagination for the past century and a half. Now Canadian researchers are facing a crucial decision on whether to relaunch attempts to find new clues about the ships’ fate.

Over the past few years they have already recovered hundreds of artefacts – from shoes and ceramic dishes to a ship’s bell and a lieutenant’s epaulette – from the wrecks of the two ships after they sank in the Canadian Arctic.

But last year marine archaeologists had to abandon dives to the wrecks because of the Covid pandemic and they are unsure if they will be able return to the ships this summer when the sea ice retreats sufficiently to allow access to the wrecks near King William Island.

Franklin set off from Greenhithe in Kent in 1845 to find the Northwest Passage, a polar route to the Far East. His ships were fitted with steam-driven propellers to help them manoeuvre in pack ice and their holds were filled with a three-year supply of tinned provisions. It was one of the best-equipped marine expeditions of its day. So what befell the ships?

From their first disappearance the mystery of the Erebus and the Terror has gripped the public’s imagination. As Andrew Lambert says in his biography, Franklin, Tragic Hero of Polar Navigation: “At the heart of every story about the Arctic stands John Franklin.”

Charles Dickens, Wilkie Collins, Jules Verne and Mark Twain all wrote about the expedition. However, the screening of The Terror on BBC Two this month has regalvanised interest across Britain and taken viewers on board the two ill-fated ships to see what life would have been like for the crew who had to endure temperatures of minus 50C throughout several Arctic winters.

With both vessels trapped in pack ice, this grim tale – based on Dan Simmons’s bestselling 2007 novel – charts not just a journey across the icy Arctic wastes but also traces the conflicts that flared between those in charge. Crucially, the script also pays due attention to the culture of the local Inuit people, something that was often disregarded by Royal Navy adventurers who later tried to find Franklin and his men.

Francis Crozier who commanded HMS Terror, is played by Jared Harris (recently in Chernobyl) as the more cautious seaman who attempts – despite a debilitating alcohol dependency – to persuade Franklin (played by Ciarán Hinds) to abandon his mission as being too dangerous. Other key characters include the ambitious first officer of Erebus, James Fitzjames (Tobias Menzies), and Henry Goodsir, known as Harry, a kindly Scottish surgeon and naturalist (Paul Ready).

Much of the drama follows Simmons’s fictional conjecture that the division in the crews’ loyalties contributed to the eventual failure of the expedition, although supernatural elements also pepper the plot. The drama has been widely praised for its production and convincing depictions of the Arctic, which were recreated digitally using the same special effects that series producer Ridley Scott used in his film The Martian.

However, for all its televisual sophistication, The Terror does not answer the key question: what really doomed the Franklin expedition? Many theories have been suggested: the crews were struck down by botulism; they suffered lead poisoning from the poorly sealed tins of food; or were badly led by Franklin, who let his ships sail on a route frequently blocked by ice even in summer. What is known is that surviving crewmen eventually abandoned both vessels and headed south on foot across King William Island. Cut marks on skeletons make it clear some indulged in cannibalism before perishing.

Just why the expedition went so badly wrong is unclear but our understanding would be transformed by paperwork, says Claire Warrior, a senior curator at the National Maritime Museum in London – and that is the real hope of the dives that will eventually start again this year or next.

“If papers on the Erebus and Terror had been kept in sealed boxes or drawers, they may have survived immersion in the very cold, dark waters,” she said. “Diaries or written commands would make the most meaningful difference in terms of understanding what happened. That is what we are hoping will be found.”

In the end, the bodies of more than 30 crewmen from the ships were found on King William Island. Most are still buried there, although two were returned to Britain. Lieutenant John Irving was identified from personal effects and was buried in Dean cemetery, Edinburgh, in 1881.

The second was initially identified as being that of Henry Le Vesconte, a lieutenant on Erebus, before it was interred beneath the Franklin memorial at Greenwich Old Royal Naval College in London. However, in 2009, the memorial was moved, and a facial reconstruction from the remains was carried out – and produced a close match with a surviving daguerreotype of Henry Goodsir. For good measure, isotope analysis of tooth enamel suggested an upbringing in eastern Scotland (Goodsir was raised in Fife) but not with Le Vesconte’s upbringing in southwest England. The remains are now attributed to Goodsir.

“Obviously we would like clues in future years to what happened to all these men but on their own, the items that have been recovered have transformed our appreciation of how they lived,” added Warrior.

“Bits of accordion, pipes and books have been found. These are touchstones to those lives and they have incredible poignancy.”

The 1680s Royal African Company trader – seen as a burial ground of slaves who perished on its final voyage – lies on the seabed about 40 miles south of Land’s End. It is being “pounded into oblivion” by “bulldozers of the deep”, claimed a leading British marine archaeologist.

This was a trade that saw more than 12 million Africans taken across the Atlantic in 45,000 voyages over 400 years. Many did not survive the journey. Any submerged evidence offering insights into untold horrors that the slaves had endured on board such ships will be lost for ever, warned Dr Sean Kingsley. He has been alarmed by underwater footage filmed for a new documentary series about the transatlantic slave trade. It reveals extensive damage to a wreck that was once “a beast of a ship”, carrying 48 cannon, perhaps 600 tons in capacity and manned by a crew of 70.

He said: “Fifty years ago, this wreck must have been a thing of wonder. Today, what’s left is tragic. Trawlers dragging nets for fish and scallops have bulldozed everything. Cannon have been dragged 300 metres away. If trawlers can throw two-ton guns around like matchsticks, then the wooden hull and small finds have no chance. Archaeologists call deep-sea wrecks time-capsules. This wreck looks like a war zone.

“Wrecks should be used as museums for memory and education. In this case, the future’s chances of bearing witness to the horrors of the slave trade are fading fast. It’s a double tragedy.”

The footage was filmed for Enslaved, a documentary about the transatlantic trade, which begins tonight on BBC Two. Kingsley, who has explored more than 350 shipwrecks, is adviser to the documentary. As the founding editor of Wreckwatch, the world’s only magazine dedicated to the sunken past, he will publish the new evidence in the next issue.

The wreck lies 110 metres down, and the Enslaved team became the first to visit it. The team included Diving With a Purpose, a group dedicated to the maritime history of African Americans.

Kramer Wimberley, its lead instructor, said: “The story of the slave trade is world history. England was involved in it, Portugal, the French and Dutch were involved in it, the Africans were involved in it. It’s a world shame. If that wreck’s the final resting place of some of my ancestors, then it’s a burial ground. But it’s also a crime scene because they were taken. There was an injustice that took place, and no one has ever been brought to account. I want justice for those people. Archaeology can make sure we never forget.”

The ship was among more than 500 despatched by the Royal African Company to West Africa between 1672 and 1713. In conducting research for Enslaved, Kingsley studied 279 of the company’s sea voyages between 1672 and 1690. He found that, of 65,411 Africans trafficked to the Caribbean, 14,668 died at sea, having been chained in cramped hulls: “Most of the Africans were seized in Whydah in Benin, Calabar in Nigeria, Gambia and the Gold Coast in modern Ghana. The enslaved ended up sold to plantation owners in Barbados, Jamaica, Nevis, Virginia and Antigua.”

Set up by the royal Stuart family, the company’s governor was James, Duke of York and future king of England, and its deputy governor was Edward Colston, whose statue was recently toppled in Bristol.

Expressing sympathy for fishermen working under harsh conditions, Kingsley criticised the inability to protect rare wrecks that lie outside UK territorial waters as “a serious heritage failure”.

The remarkable haul points to a history of highly charged ceremonies in which the elite of the region’s Tiwanaku state boated out to the reef and sacrificed young llamas, seemingly decorated for death, and made offerings of gold and exquisite stone miniatures to a ray-faced deity, as incense billowed from pottery pumas.

Tiwanaku state arose in the Lake Titicaca basin, around the border of modern Bolivia and Peru, between the 5th and 12th centuries AD, and went on to become one of the largest and most influential in the Andes. Formed by a natural fault that divides the Andes into two mountain ranges, the basin is a unique ecosystem with an “inland sea” set 3,800m above sea level. At the time of the Spanish conquest, the basin was home to an estimated 1 million people.

Marine archaeologists decided to explore the Khoa reef after amateur divers found a number of ancient items at the site. The reef is submerged in more than 5m of water about 10km off the northwestern tip of the Island of the Sun, a central feature of Lake Titicaca.

The researchers excavated a trove of artefacts including a lapis lazuli puma figurine and other miniature stone animals, ceramic puma incense burners and gold ornaments including engraved sheets, a medallion, and an L-shaped piece marked with puma and condor silhouettes. Perforated gold leaves still attached to fragments of leather may have been used to make ear tassels and other regalia to dress young llamas killed in the ancient ceremonies, the researchers believe.

Taken together, the items reveal how the lavish ceremonies displayed and disposed of the most prestigious materials that money could buy in the ancient Andean empire. Besides the gold and the carved and polished stones were spiny oyster shells from the warm waters off the Ecuadorian coast, nearly 2,000km away. They could only have been obtained through trade.

“What is great about these artefacts is that, beyond their beauty and the quality of manufacture, they were discovered in an undisturbed context,” said Christophe Delaere, a marine archaeologist at the University of Oxford and the Free University of Brussels. “This is one of the advantages of underwater heritage. Lake Titicaca protects its ancient material culture from time and man. Never before have so many artefacts of this quality been discovered. The history that these objects tell us is exceptional.”

Found alongside the artefacts were llama bones and the remnants of burnt fish, the latter of which are thought to have been eaten during the ceremonies. Carbon dating of charcoal and bones at the site found that the offerings were made throughout the 8th and 10th centuries AD, according to a report in the Proceedings of the National Academy of Sciences.

The ancient offerings are not the first riches to be recovered from Lake Titicaca, but the exceptional quality and abundance of the items puts the reef at the heart of the Tiwanaku people’s beliefs and ritual landscape.

One of the major questions surrounding Tiwanaku state is how it expanded so effectively across the Titicaca basin in the first millennium. Charles Stanish, an anthropologist on the team from the University of South Florida, said that pilgrimages leading up to elaborate ceremonies were a crucial part of the state structure. Through ritual, religion and “supernatural punishers”, the state encouraged cooperation and deterred freeloaders and other rebels.

“What we’ve discovered in the Titicaca basin are pilgrimages and ritual processions and these are part of the state apparatus. As you participate in them you are reinforcing the power of the state,” Stanish said. “Combined with what’s been found off other islands in the 1990s, the discovery of these items on the reef shows us there was probably a series of pilgrimages or precessions around the lake and I find that to be extremely exciting.”

More than a dozen Tiwanaku sites have been found on the Island of the Sun. One, near the north-west shore, is a puma-shaped ceremonial complex. But from Khoa reef, those taking part in a water ceremony would have a panoramic view of the lake and the spectacular surrounding mountains. “It is not surprising that the Tiwanaku elite appropriated this space for costly and highly charged ceremonies,” the authors write.

“Ritual and religion were profoundly important in ancient states. It is not some new age-y thing,” said Stanish. “Ritual and religion structured people’s lives, it structured the economy and the whole of society. This is how these people were able to create spectacular ways to get along and have a very successful society.”

Over the following four centuries, as Spain’s maritime empire swelled, peaked and collapsed, the waves on which it was built devoured hundreds of ships and thousands of people, swallowing gold, silver and emeralds and scattering spices, mercury and cochineal to the currents.

Today, three researchers working for the Spanish culture ministry have finished the initial phase of a project to catalogue the wrecks of the ships that forged and maintained the empire.

Led by an archaeologist, Carlos León, the team has logged 681 shipwrecks off Cuba, Panama, the Dominican Republic, Haiti, Bermuda, the Bahamas and the US Atlantic coast.

Its inventory runs from the sinking of the Santa María to July 1898, when the Spanish destroyer Plutón was hit by a US boat off Cuba, heralding the end of the Spanish-American war and the twilight of Spain’s imperial age.

After spending five years scouring archives in Seville and Madrid, León, his fellow archaeologist Beatriz Domingo and the naval historian Genoveva Enríquez have put together a list aimed at safeguarding the future and shedding light on the past.

“We had two fundamental objectives,” says León. “One was to come up with a tool that can be used for identifying and protecting wreck sites – especially in areas where there’s a high concentration of sunken ships.

“The other was to recover a bit of history that’s been very much forgotten. The most famous ships have been investigated, but there’s a huge number about which we know absolutely nothing. We don’t know how they sank, or how deep.”

The information gathered would help the team to find out what navigation was like at the time, he said.

The team’s research will thrill historians and cartographers, but is unlikely to delight those who harbour romantic notions about doubloons, parrots and Jolly Rogers.

It found that 91.2% of ships were sunk by severe weather – mainly tropical storms and hurricanes – 4.3% ran on to reefs or had other navigational problems, and 1.4% were lost to naval engagements with British, Dutch or US ships. A mere 0.8% were sunk in pirate attacks.

Archaeologists have located the remains of fewer than a quarter of the 681 vessels on the inventory to date.

León, Domingo and Enríquez were surprised to come across 12 areas with particularly high concentrations of wrecks in Panama, the Dominican Republic and the Florida Keys. Instead of the expected two or three wrecks per bay, they discovered as many as 18.

“Some of these areas, like Damas bay in Panama, are very open,” says León. “There were huge annual trade festivals there from the 16th century to the mid-17th and that attracted a massive amount of maritime traffic. It’s not a very protected area and so when a storm came in, the ships sank.”

Or, to put it in more modern terms: “It was like a motorway. It’s not very deep there, either. And ships are a bit like aeroplanes. They usually go down on take-off or landing.”

Treasure hunters tend to be more interested in ships that came to grief on their way back from the Americas, but León and his colleagues say the ill-fated outward-bound vessels are just as compelling.

“The cargo they carried speaks of a massive amount of trade,” says the archaeologist. “But it’s not just about products and trade. These ships were also carrying ideas. We were surprised to find a lot of boats loaded with religious objects – relics, decorations and even stones to build churches.”

Their findings, however, go beyond cutlasses and crucifixes, and help to explain how Spain succeeded in enriching itself for centuries.

As well as the “tonnes and tonnes” of mercury sent to the new world to be used in extracting gold and silver from the mines that fed the empire, “we found boats that were carrying clothes for slaves”. Others carried weapons to be used in putting down local rebellions.

The researchers now plan to transfer the paper inventory to a database that the Spanish government can share with countries with colonial shipwrecks in their waters. León hopes the information his team has gathered will give those countries what they need to safeguard their maritime heritage against unscrupulous treasure hunters who all too often use salvage permits as a cover for more profitable explorations.

“We have to be very careful about the details and positions of some of the ships,” he says. “But the ministry works with countries that have ratified the 2001 Unesco convention [on the protection of the underwater cultural heritage], so they should be countries that aren’t going to use this information to make deals with treasure-hunting firms.”

Anyway, he adds, the big treasure-hunting outfits will not be interested in most of the wrecks on the inventory. “It’s true that the big treasure-hunting firms have spent years doing what we’ve been doing, but only when it comes to the ships that carried huge treasure loads. I don’t think we’d be helping them out much, to be honest.”

The three researchers are now preparing for another deep dive, into the archives and libraries. The Spanish empire was, after all, a very, very large one. “We’ve still got many more areas to go,” says León. “Next year, I’d like to work on Mexico, Colombia, Puerto Rico and Costa Rica so as to kind of finish up the Caribbean area. After that’s it’s on to the Pacific.”

Divers found the right arm, encrusted and stained green, under half a metre of sediment on the boulder-strewn slope where the ship and its cargo now rest. The huge vessel, perhaps 50m from bow to stern, was sailing from Asia Minor to Rome in 1BC when it foundered near the tiny island between Crete and the Peloponnese.

The project team, from the Greek Ephorate of Underwater Antiquities and Lund University in Sweden, discovered the buried arm with a bespoke underwater metal detector which has revealed the presence of other large metal objects nearby under the seabed. “There should be at least seven statues,” Alexandros Sotiriou, a Greek technical diver on the team told the Guardian. The operation is overseen by Ageliki Simosi, director of the Greek Ephorate of Underwater Antiquities, which is responsible for all underwater archaeology in Greece.

“What we’re finding is these sculptures are in among and under the boulders,” said Brendan Foley, co-director of the excavations team at Lund University. “We think it means a minimum of seven, and potentially nine, bronze sculptures still waiting for us down there.” The boulders that overlie the metal objects weigh several tonnes and may have tumbled onto the wreck during a massive earthquake that shook Antikythera and surrounding islands in the 4th century AD.

The bronze arm, probably from a statue of a male, is the highlight of the team’s 2017 excavation season. Among other objects the divers recovered are a patterned slab of red marble the size of a tea tray, a silver tankard, sections of joined wood from the ship’s frame, and a human bone. Last year, the team found the skull, teeth, ribs and other bones of an individual who perished on the wreck. They have since extracted DNA from the skull and from it learned the individual’s sex and where they came from. Until those results are published, the person is known as Pamphilos after divers found the name, meaning “friend of all”, carved on a buried cup that had been decorated with an erotic scene.

The Antikythera wreck first came to light in 1900 when Greek sponge divers happened on the scene in 50 metres of water. Archaeologists have since pulled up spectacular bronze and marble statues, ornate glass and pottery, stunning pieces of jewellery, and a remarkable geared device – the Antikythera mechanism – which modelled the motion of the heavens. During the 2017 excavations, divers recovered a bronze disc that may be a missing part of the ancient device.

But it is the statues that made the wreck famous. In the 1900s, archaeologists working at the site surfaced pieces of a beautiful Hellenistic bronze, named the Antikythera Youth. The statue now stands in the National Archaeological Museum in Athens alongside an impressive bronze head named the Antikythera philosopher, also hauled from the wreck. Both date to the 4th century BC, raising the question of how they came to be aboard the ill-fated ship 300 years later.

Jens Daehner, associate curator of antiquities at the J Paul Getty Museum in Los Angeles, said the Antikythera wreck had already yielded significant bronze statues. “The chance to recover another group of lifesize statues associated with the wreck is extraordinary, because bronzes are usually encountered randomly under the sea, picked up by fishing nets or chanced upon by divers,” he said. “Those finds are not excavated like at Antikythera, where archaeologists can and do document the entire context, which provides all the sorts of very valuable data as to when the sculptures were transported and why they were on the ship: for trade, as booty, or as scrap metal to be recycled.”

The bronze recycling industry was huge in classical times and later in the medieval period, leading to the destruction of countless statues and other artefacts that would be priceless today. For this reason, many of the finest specimens of bronze statues that survive were once lost at sea. “Ancient bronze sculpture in general is rare due to the metal having been recycled in antiquity and later. We think of the ones from the sea as those that got away,” said Daehner. “Any chance to recover more Greek sculptures in any medium, but particularly in bronze, should not be missed.”

To recover the statues will take a massive effort. The divers must first remove boulders that are in their way, either by hauling them up, or by drilling holes in the rocks and filling them with grout that expands to fracture the stone. Another option is to crack the boulders open with small shaped charges that technical divers use to rescue people trapped when undersea caves collapse. But even if the statues can be lifted from the sea, they will be broken and need costly and time-consuming conservation and reconstruction.

Statues are not the only objects the excavators hope to find. The latest excavations uncovered a lump of material bearing a bronze disc that matches the size of geared wheels found in the Antikythera mechanism. Wound by a handle, the device showed the movement of the sun, moon and planets in the sky, but not all of the machine was recovered. “The disc looks very exciting indeed,” said Andrew Ramsey, a CT specialist at Nikon Metrology in Tring, who used CT scans to read inscriptions on the original pieces of the mechanism. But the disc may be something entirely different. Preliminary x-ray images reveal no teeth, but an image of a bull, suggesting the disc is not a cog but a decorative item.

Mike Edmunds, emeritus professor of astrophysics at Cardiff University and a member of the Antikythera Mechanism Research Project, said the findings are impressive. “They are getting very good at detecting bronze items which raises the possibility that they may be able to find either the missing planetary gearing from the Antikythera mechanism, which we know is there from the analysis of the inscriptions on the mechanism, or a new piece of mechanism, or another mechanism that was being transported, and that would be very exciting.”

The team will return to the wreck in the spring, optimistic that they may pull up fresh treasures from the wreck. “It’s not going to be just the bronze sculptures,” said Foley. “We’re down in the hold of the ship now, so all the other things that would have been carried should be down there as well. Every day is going to be like opening Tut’s tomb.”

The village that once sat on the Mediterranean coast now lies 10 metres beneath the waves off Israel’s shore. It was inundated when sea levels rose at the end of the last ice age. But Atlit-Yam was destroyed before then, and swiftly, perhaps by a tsunami. Buried under sand at the bottom of the sea, it now ranks as the largest and best preserved prehistoric settlement ever found on the seafloor. Human skeletons still lie there in graves, undisturbed.

For marine archaeologists, Atlit-Yam is a trove from the Neolithic world. Research on the buildings, tools and the remains of past lives has revealed how the bustling village once worked. “It looks as though it was inhabited until the day it was submerged,” said Benedetto Allotta, head of industrial engineering at the University of Florence. But for all the secrets the site has shared, it is only one window into a lost world. For a fuller picture, researchers need more sunken settlements. The hard part is finding them.

In January, work will start on a new project to transform the search for sunken cities, ancient shipwrecks and other subsea curiosities. Led by Italian researchers, Archeosub will build a new generation of robotic submarines, or autonomous underwater vehicles (AUVs), for marine archaeologists. “You can find plenty of human settlements not far from the coast,” Allotta said. “In the Mediterranean there will be a lot more Atlit-Yams waiting to be explored and studied.”

The goal of Archeosub is to put sophisticated AUVs in the hands of cash-strapped researchers. That, in part, means turning the costly, heavy technology of the military and oil industries into far cheaper and lighter robots. They must be affordable for archaeological organisations and light enough to launch by hand from a small boat, or even the shore, rather than from a winch on a large research vessel.

Slashing the cost and weight is only the start. The team behind Archeosub has begun to make the AUVs smarter too. When thrown overboard, the submarines can become part of an “internet of underwater things” which brings the power of wifi to the deep. Once hooked up, the AUVs can talk to each other and, for example, work out the most efficient way to survey a site, or find particular objects on the seabed.

Field tests show the approach can work. When cargo ships near Porto in northern Portugal lose containers overboard, AUVs can be deployed to find the missing goods. And in a trial last year, Allotta’s group sent three AUVs to search for wrecks at Marzamemi, off the Sicilian coast. The site is the final resting place of a Roman ship, known as the “church wreck”, which sank while ferrying pre-formed parts of marble and breccia for an early Christian church in the 6th century AD. “We used the AUVs to pass through and look for new ruins,” Allotta said. “We could do a reconstruction of the area, where old Roman ships sank while bringing marble columns to Italy,” he said.

Creating an internet beneath the waves is no breeze. Slip under the surface and the electromagnetic waves used in wifi networks travel only centimetres. Instead, a more complex mix of technologies is called for. Acoustic waves, which are affected by depth, temperature, salinity and surface wind, are used to communicate over long distances underwater. At close range, AUVs can share data over light beams. But more creative solutions are also envisaged, where an AUV working on the seabed offloads data to a second which then surfaces and beams it home by satellite link. Work is underway on AUVs that can beam pictures from the seabed over acoustic waves, and dock with others that charge them up. Surface buoys that receive GPS signals tell the AUVs where they are.

“If you want to build an internet of underwater things, you cannot use the technology we have developed for the terrestrial world,” said Chiara Petrioli, a computer engineer who leads the work under the Sunrise project at Rome University. “You have to be smarter.”

David Lane, a professor of autonomous engineering at Heriot-Watt University in Edinburgh, has created a marine version of Dropbox for the underwater internet of things. It allows AUVs to share information from seafloor scans and other data. So if an AUV on a first pass survey spies an intriguing object on the seabed, it can share the coordinates with a nearby AUV that carries better cameras and sonar, and arrange for a closer inspection once it has left the area.

“The use of these vehicles has huge potential for marine archaeology,” Lane said. “There’s a lot of history wrapped up in what’s lying on the seabed.”

One site where Allotta plans to deploy the new AUVs is the Gulf of Baratti off the coast of Tuscany. In 1974, a remarkable shipwreck was discovered there in 18 metres of water. More than a merchant ship, the 2000-year-old vessel was a travelling medical emporium. More than 100 wooden vials were found on board, along with other ancient medical supplies, including tin containers of tablets that may have been dissolved and used as eyewash. Other Roman ships went down in the waters, shedding cargoes of olive oil and wine held in huge terracotta pots called dolia. Often it is only the dolia that remain, the wooden ships lost, or at least buried, under silt.

Allotta hopes to have the first test results from the Archeosub project in the summer. “Right now, we don’t have the right technology to give to archaeologists,” he said. “But we are close.”

It takes an effort of imagination to conjure this place back to its ancient flourishing before its abandonment in the seventh century. But once it was a city with perhaps 16,000 inhabitants, full of temples to gods such as Hera, Aphrodite and the Dioskouroi (Castor and Pollux), and dominated by a vast sanctuary dedicated to the Egyptian deity Amun-Ra, from which a sphinx-lined avenue led to the Canopic branch of the Nile, which long ago flowed here.

There was also a Hellenion, a sanctuary dedicated to all the gods of the Greeks: an early expression of pan-Hellenic identity from the politically independent city-states that, according to the historian Herodotus, jointly founded the city at the invitation of the pharaoh. The Greek temples started off as simple affairs, sacred enclosures with outdoor altars, but pedimented structures were built once the Greeks had learned the knack of building colonnaded temples from the Egyptians. Surrounding the sanctuaries were mud-brick houses several storeys high, some with dovecotes on their roofs. The same kind of conical pigeon houses can be seen in the villages today.

All Mediterranean traders who had dealings with Egypt – not just Greeks, but also Phoenicians, Cypriots, Levantines – were obliged to come to Naukratis to trade their oil and wine and pay their tax, sailing more than 40 miles inland down the Nile via Thonis-Heracleion, a sister port at the mouth of the river on the Mediterranean. (That port was overwhelmed in antiquity by the encroaching sea: impressive finds have been made by marine archaeologists, which can also be seen in the British Museum exhibition.)

After the traders had done their deals, there was entertainment to be had: Herodotus tells us that Naukratis was famous for its excellent courtesans. Charaxos, the brother of the poet Sappho, came here on trading trips from Lesbos and so completely lost his heart to the beautiful Rhodopis that he bought her her freedom; she became fabulously rich.

Ross Thomas, who is directing the dig, walks me round the excavations, just a couple of days into the 2016 season, their fifth. No monuments remain, nor yet a whiff of the gorgeous Rhodopis, and yet the past is palpable. He points out a jalabiya-clad man sitting outside his house on a classical column base; and the recently ploughed fields are full of ancient potsherds. Ashraf Abdel-Rahman, a local official of the Supreme Council of Antiquities, picks up a piece. Thomas gives it a casual glance. “Fourth-century BC mushroom amphora, imported,” he says, with impressive taxonomical ease, and chucks it back.

We meet Ben Pennington, a geoarchaeologist who, with young Egyptian trainees, is sinking an auger nine metres below the surface in order to glean information about the area’s ancient topography and environment. In another field, Eleanor Maw is in charge of a team surveying fields using the technique of magnetrometry – “basically, a non-invasive way of looking at what’s underneath”, she explains, through which she can chart the outlines of the old mud-brick tower houses. Another team is digging in a pair of trenches that may pinpoint the entrance to the Hellenion.

Yet another group, perhaps most excitingly, is working at the edge of where the Nile once flowed. Naukratis has been partially excavated before, first by the great Flinders Petrie in the 1880s. (He realised he’d stumbled across the city when he read a Greek inscription saying so – it was built into the house he was staying in. “I almost jumped as I read,” he wrote in his journal. “So this is Naukratis!”). The course of the river, however, was established only by Thomas’s team, and he is excited at the prospect of discovering the quayside and, perhaps, well-preserved boat remains. It is highly possible, for the site is waterlogged, providing the anaerobic conditions that slow the decay of wood.

Today, though, the haul is potsherds from the sixth century BC. Most of them – bright reddish, sandy to the touch – are locally made Egyptian wares. There are also Greek mortaria – bowls for pounding ingredients into sauces – and all manner of wine amphorae from the east Greek world, the Hellenic cities on what is now the west coast of Turkey. Thomas and his colleague from the British Museum, Alexandra Villing, sort through them. Petrie and his Victorian successors tended to ignore the Egyptian pottery finds, leading to a skewed vision of what kind of cultural texture this city might have had. Ross and Villing suspect the interaction and cultural exchange between people here was richer and more complex than had been believed. “It’s not a Greek colony,” says Thomas. “It’s a mixed community.” (The other matter over which Flinders Petrie discreetly drew a veil was the vast number of little terracotta figures of Harpocrates, the child of Isis and Osiris, that he found around the city. The figurines had comically vast and engorged phalluses, associated with the god’s role in ensuring the land’s fertility.)

There is no more impressive evidence of the cultural encounters that occurred at Naukratis than in the Egyptian Museum, in Cairo, which Villing and I visit together. We are looking for a statue. Pass it by and you’d probably take it for another pharaoh: the four-metre-tall figure has an Egyptian ruler’s kilt, rigid arms and left foot striding forward. He’s not one, though: he was erected in the temple of Amun-Ra in Naukratis in around 300BC (a generation after Alexander’s conquest), and his name, according to the hieroglyphs on his back, is Horemheb. So far, so Egyptian, but the inscription goes on to tell us in no uncertain terms that “I am a Greek” – and that his father was Krates, a very Hellenic name, and his mother was the Egyptian-sounding Shesemtet.

There is a lot of this intriguing cultural mingling in Egypt, and it runs right through to the Romans. In the catacombs of Kom el-Shoqafa in Alexandria, a Roman family is buried in an elaborate tomb arranged like a pedimented temple with niches for the sarcophagi, which are decorated with flower garlands and tragic masks – altogether very classical. But the pediment is carved with Egyptian falcons, the Roman couple are depicted as Egyptian from the neck down (another kilt and striding left leg) and the relief carvings above their tombs are of Egyptian scenes, including Anubis presiding over a mummification. Nearby, in the sanctuary below the temple of Serapis – a Greek-friendly version of Osiris – the Roman emperor Hadrian dedicated an extraordinary, lifesize bronze bull representing the Egyptian god Apis. A replica is in situ, but the original can be seen in the British Museum exhibition.

Sometimes it’s bewildering even to attempt to follow these cultural and religious currents as they eddy and flow around the Mediterranean. A pottery object excavated by Petrie in Naukratis, which is about to tour to museums around the UK, also tells a complex tale. “He’s a mid-sixth-century figure of a man carrying bow and arrows, with two hares and two boar piglets on his shoulders,” explains Thomas. “He’s wearing a Cypriot cap, an Egyptian kilt and a shirt. The inscription says, ‘Kallias dedicated me to Aphrodite’. We think the dedicator was probably an east Greek.” In other words, it was made in Cyprus in an Egyptian style, where it was bought and inscribed probably by a Greek trader from Ionia (now Turkey), and then dedicated in a Greek temple in Egypt. There’s a story that comes from the second- and third-century AD author Athenaeus, born in Naukratis, which chimes uncannily accurately with the journey of that votive figure. He tells of a Greek trader from Naukratis who, on his way back to Egypt, bought a figurine of Aphrodite from Paphos on Cyprus. On the way home, he was caught up in a storm and prayed to the goddess. She answered him: the storm calmed and a myrtle bush miraculously sprouted on board. When he arrived in Naukratis, he dedicated his figurine at the temple of Aphrodite and hosted a feast, the guests crowned with myrtle wreaths.

In the Naukratis of 2016, there’s a breath of excitement: Ashley Pooley’s team, working at the ancient riverbank, has found some wood, preserved here in the mud since the sixth century BC. It’s not a stern or a prow, but it’s something; perhaps, they think, part of a quayside boardwalk. Not bad for day two in the field – and a hopeful sign that the fertile black soil of Egypt has more and more knowledge to impart.

• Sunken Cities: Egypt’s Lost Worlds is at the British Museum, London, 19 May-27 November.

It must be remembered that it is our cultural attachment that will be doing the dredging, our obsession and fascination with these objects that circulate as evidence of the all-powerful histories of empire. Where we decide to put Cook’s ship and its contents will shape where it takes us. Through its presentation we will relate to it culturally; as an object of desire or fascination for some, and boredom for others. We will tell a new story and it will make us feel something.

Many of the Anglo-American and Australian public are likely to feel awe in the presence of the Endeavour. As we stand before it, in whatever state it is in (probably not wrecked but reconstructed to its “original” form), it is unlikely to rouse anything like the grief that has ripped the souls of millions of Indigenous Australians. Especially if we preserve it, present it and interpret it as part of the British Museum’s set.

This is not to say that the ship should become an opportunity for apology or sympathetic feeling. In Australia many Indigenous activists, public intellectuals and academics tell us that they aren’t interested in sympathy or other paternalistic emotions – an attitude that will be no surprise to those familiar with public forums such as the Guardian column IndigenousX.

Which should not be to dismiss the historical value of saying sorry, either. And it certainly isn’t to speak on behalf of Indigenous people – as if I ever could. It is merely to say that we are all looking forward as well as back, that life is moving on despite us, and we need to move things on too, in a way that changes the story. A story that until now has been that of “the famous British explorer”. A story that is in fact one of colonial rule, whiteness, and Indigenous sovereignty. A story in which we are all intertwined.

There is no such thing as “this side of the world”. The world isn’t made up of sides. Australia is very much “here” – Britons hear the accents, buy the products, watch the TV. And we are very much “there” – we fill the tourism ventures, go backpacking, populate their ABC with our BBC. We export our media. And in return Australia gave us The Conversation.

The resurrection of Cook’s ship is taking place here, in our shared world; the one without sides. This is why much academic literature refers to the colonial past as a “present”, to recognise how what is happening now continually remakes the effects of the past.

Perhaps what should be most worrying is that the Rhode Island Marine Archaeology Project “is launching a campaign to finance the construction of a storage facility to accommodate the objects”. Is it so hard to imagine that the ship should be placed in the hands of a co-operative of First Nations organisations rather than stay with those that will pander to a whitewashed version of history? As ever, we entrust our history to scientists, sometimes governments and corporations, rather than to those who produce counter-narratives that could unsettle our place in the world.

How we choose to open up the Endeavour to modern interpretation will dictate how much opportunity there is for new stories to be told, for the familiar narratives of a heroic Captain Cook to be subverted by the imperialistic reality.

It is hard not be cynical about the possible resting place for this famous old ship. My girlfriend jokes about an auction on eBay. I have a vision of a jolly theme park, Cook’s vessel digitally mediated with fancy holograms, all the better to distract from the reality of the Endeavour’s colonial past.

But the ship that saw so many adventures was sold, forgotten and lost. For centuries, the fate of HMS Endeavour has remained a mystery.

Now marine archaeologists are almost certain they have found its wreck at the bottom of the sea – off exotic Rhode Island.

Researchers with the Rhode Island Marine Archaeology Project (Rimap) will announce on Wednesday that they are nearly sure that they have found the Endeavour, the ship that Cook captained on his voyages to New Zealand and Australia.

“We usually don’t make any announcement as we keep working away until we have something significant to say,” Dr Kathy Abbass, principal investigator, said. “We may say, ‘we think we found the Endeavour,’ well, yeah. Now I have to prove it.”

Admiralty documents detailing the Endeavour’s dimensions have led Abbass to believe that the ship, built like a sturdy commercial vessel to carry survival and scientific cargo on a long voyage, was sold into private hands in 1775 and renamed Lord Sandwich – the first lord of the admiralty at the time. When the 13 American colonies revolted a year later, it was leased back to the British navy as a troop transport for British and Hessian soldiers, and then used as a prison ship in Newport Harbor, Rhode Island, during the war.

Rhode Island was the first state to disavow its loyalty to King George III, exactly two months before the 13 colonies formally issued the Declaration of Independence.

By late August 1778, American forces had besieged Newport, and were hoping the French navy could help them oust the British from the harbor town. The British decided to scuttle 13 other ships, Lord Sandwich among them, to stymie the French navy en route. A world away its former captain had crossed the Bering Sea into the Arctic Circle and was hunting walruses for food and oil. He would die only a few months after his most famous ship was wrecked.

Abbass’s team, working with Australian researchers, have mapped nine of the 13 sites where the ships were scuttled. Five of those ships were wrecked in an arc, near the modern Naval War College to the north and in the waters by Brenton Cove to the south. The researchers have mapped four.

“We think we have a really good chance to close in on the fifth one,” Abbass said, noting a recent analysis of remote sensing data on the harbor.

In a statement, Rimap said it “now has an 80 to 100% chance that the Lord Sandwich is still in Newport Harbor, and because the Lord Sandwich was Capt Cook’s Endeavour, that means Rimap has found her, too.”

The researchers will next map the remaining portions of the harbor in their search for the wreck itself.

The researchers estimate that their research on 83 projects, including other revolutionary-era vessels, second world war wrecks and a reputed slave ship, has a total value of more than $5.5m. The wreck of the Endeavour would probably be their most valuable discovery yet: the first European ship to land in Australia, leading to the founding of a British colony there, and the flagship of one of Britain’s greatest explorers.

Although the Endeavour was largely forgotten by its contemporaries, its later fame has led to rumors and speculation about the ship’s fate. Some have suggested the ship survived the war, was refitted and registered as a French vessel, La Liberté, and then sunk into Newport harbor in 1794. Others believed the ship actually made it back to London, and was opened to visitors in 1825, and in the 19th century a New Zealand captain thought he found the wreck in Dusky Sound, only to be proven wrong. In 1991, when the space shuttle Endeavour was rolled out for service by Nasa, the space agency was presented with what they called “a piece of the original ship”, by the University of Rhode Island.

Abbass hopes to put the mystery of the original Endeavour’s fate to rest in the next few months, and called for a new facility to conserve, display and store some of the artifacts pulled from the underwater sites. Rimap hopes to build this facility at Butts Hill Fort, the center of where American forces stood during the battle for the colony.

The Esmeralda was one of two ships that sank in a storm off the coast of Oman in 1503, only five years after Da Gama discovered the first sea route from Europe to India.

After three years of excavation and historical and scientific research – the findings of which are reported on nationalgeographic.com – the archaeologists, which included teams from Bournemouth University and Oman’s ministry of culture, announced that they had found the site of the wreck, and with it a collection of artefacts including one of the rarest coins in the world and what may be part of a previously unknown maritime astrolabe.

David Mearns, director of West Sussex-based Blue Water Recoveries which led the expedition, told the Guardian the major significance of the find was the date of its sinking, very early in the period when a handful of European maritime powers were racing to discover and exploit new routes to the east.

“This is the earliest ship [from the period of European maritime exploration of Asia] that has been found by a long stretch,” he said. “If you consider that that pre-colonial period started on a major basis with Columbus, in 1492, this is just a decade after that.”

The ship sank in a storm off the coast of what is now the small Omani island of Al-Hallaniyah in 1503, with the loss of all crew and of its captain Vicente Sodre, a maternal uncle of da Gama.

Because it broke up in shallow waters, very little of the ship itself has survived, but thousands of artefacts were uncovered from the sand in the shallow bay. Among them was an incredibly rare silver coin called an indio, of which only one other is known to exist. The coins were forged in 1499 after da Gama’s first voyage to India, which helps date the wreckage, Mearns said. Stone cannonballs appearing to bear Sodre’s initials were also discovered.

However Mearns said the most exciting discovery was a metal disc bearing the Portuguese coat of arms and an image of an armillary sphere, a model of celestial globe, which was the personal emblem of the then King of Portugal. The archaeologists have speculated that it may be a component part of a type of astrolabe, a navigational device, but are not certain, he said.

“There’s no doubt it’s a very important object. It’s made of valuable material, it’s got these two iconic symbols on it, they don’t just stamp those things on to any piece of equipment on a ship. This was an important thing, but what was it?” He said he hoped other experts would now add their input to help identify the object.

“What’s really exciting about this discovery being so early, this may be something nobody has ever seen before, and that’s challenging for the archaeologists but also fun and exciting.”

He said the dig had been a “dream job” for the archaeologists. “These are people who work in England in dry suits in freezing cold water, sometimes they can see no further than their nose. So to come to this really beautiful island, completely remote, you have nothing there … this lovely bay, warm waters and you are visited every day by dolphins coming to play with you.

“These are the sort of exotic holidays that people would pay tens of thousands of pounds to go on.”

The findings of the expedition were published on Tuesday by The International Journal of Nautical Archaeology.

Ayoub al-Busaidi, the supervisor of marine archaeology at the Oman ministry of heritage and culture, said the dig marked the first underwater excavation carried out by his country. He said it had inspired officials to continue to explore the waters around the sultanate for other finds.

“Oman is now looking at outside archives to read about the relationships and trade between Oman and the outside world.”