After 400 years in the Virginia dirt, the box came out of the ground looking like it had been plucked from the ocean. A tiny silver brick, now encrusted with a green patina and rough as sandpaper. Buried beneath it was a human skeleton.

The remains would later be identified as those of Capt. Gabriel Archer, one of the most prominent leaders at Jamestown, the first permanent English colony in America.

But it was the box, which appeared to be an ancient Catholic reliquary, that had archaeologists bewildered and astonished. “One of the major surprises was the discovery of this mysterious small silver box,” said James Horn, the president of the Jamestown Rediscovery Foundation. “I have to say, we’re still trying to figure this out. You have the very strange situation of a Catholic reliquary being found with the leader of the first Protestant church in the country.”

The finding is a historical bombshell, unearthed in a grave on the site of what was once the first church built at Jamestown. Which means researchers may have just discovered proof of an underground community of Catholics — including Archer and perhaps the person who buried him with the relic — who pretended to be Protestants.

Researchers may have just discovered proof of an underground community of Catholics — including Archer and perhaps the person who buried him with the relic — who pretended to be Protestants.

“The first settlers there were mostly members of the Church of England,” said James O’Toole, a history professor at Boston College who focuses on the roots of American Catholicism. “While they didn’t have the same active hostility to Catholics that the slightly later Puritan colonists in New England did, they were not particularly welcoming to Catholics. If there were Catholics in Tidewater Virginia … that would be news.”

It’s the kind of discovery that makes historians, anthropologists, archaeologists, and other academics giddy with curiosity. But it raises even bigger questions, too—ideas that could rewrite our understanding of the intersection of religious and cultural identities in colonial America.The English settlement of the New World is most often remembered as a Protestant endeavor. But if indeed there were Catholics at Jamestown, then, from the very beginning, it was a project pursued by those of multiple faiths, seeking new opportunities.

“There is this sense that American Catholic history begins in the 19th century with a wave of immigrants from Germany and Ireland in the 1820s and 1830s, but there is a history of earlier Catholicism,” said Maura Jane Farrelly, an associate professor of American studies at Brandeis University. “What’s captivating about it is the notion of the secretive nature. If he’s secretly Catholic, what does that faith mean to him that he’s willing to hold onto it even though it’s dangerous?”

“We have been finding bits and pieces of rosaries and crucifixes and other things that obviously were Catholic.”

Researchers believe the box was buried with Archer after his death between 1608 and 1616—which would mean the person who buried him would have known the significance of the artifact. Archaeologists and historians announced their discovery Tuesday at the Smithsonian, along with the identities of three other key Jamestown leaders whose remains were buried nearby.

All four men were “involved in all of the major decisions that took place during the first four years of the colony’s history,” Horn said in a video about the discovery. Researchers sussed out their identities from a list of several dozen high-status men who could have died in the early 1600s — a particularly chaotic period at Jamestown that included what’s known as “the starving time,” a grueling winter when three-quarters of the colonists died, and some resorted to cannibalism.

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Along with Archer, researchers found the remains of the Rev. Robert Hunt, the first Anglican minister at Jamestown; Sir Ferdinando Wainman, a high-ranking officer who was in charge of horses and artillery for the colony; and Capt. William West, a nephew of the governor of the Virginia Company that funded the establishment of Jamestown and other colonies in the New World.

The presence of the relic in Archer’s grave also calls into question some of what researchers previously believed — their understanding of Archer as an individual, and of Jamestown and the trajectory of Catholicism in America more broadly.

Silver Reliquary and fragments of coffin wood found in the grave of Gabriel Archer. (Jamestown Rediscovery Foundation / Preservation Virginia)

Archer, an influential secretary and magistrate “was one of the most prominent of the first leaders at Jamestown,” Horn told me. Historians knew Archer as a rival of Captain John Smith, the explorer who, according to legend, was saved from execution by Pocahontas, the daughter of a Powhatan chief. Smith and Archer were rivals. “And Archer spent a good chunk of time trying to remove Smith from the government council of Jamestown,” Horn told me.

Researchers now wonder whether there was more to the antagonistic relationship between Smith and Archer. Could Archer’s motives — as a colonial leader, as a searing critic of Smith’s — have been linked to a secret religious identity?

“Gabriel Archer was a prime character, an eminent leader in this early period,” Horn told me. “He was taking on Smith, he’s involved in bringing down the first president [of the colony], he’s really at the heart of intrigue. I think historians have always considered that his motives were primarily personal, trying to elevate his own position. But was there something more going on? Was he trying to destabilize the colony’s leadership from within?”

This idea is stunning for a couple of reasons, the most important of which is that Jamestown was fundamentally anti-Catholic.

This idea is stunning for a couple of reasons, the most important of which is that Jamestown was fundamentally anti-Catholic. “This was a big ambition here on the part of the English,” Horn said. “Jamestown is not meant to be a fairly minor enterprise. It’s meant to be the beachhead for an English empire in America that will serve as a bulwark against Catholicism. That’s a lot of freight for this little object to carry.”

Catholicism was feared by the English, too. Settlers at Jamestown believed there was a very real threat that Spanish warships would one day arrive with Catholic conquistadors prepared to fight for the New World. Incidentally, this anti-Spanish, anti-Catholic attitude — which continued long after Archer and his townsmen died — is what, in 1632, situated the Province of Maryland where it is today, rather than farther south where its Roman Catholic founder originally wanted it to be.

“When George Calvert was campaigning to get the charter to Maryland, he was actually looking to get territory — and he was approved to get territory — in what is now North Carolina,” said Farrelly, the Brandeis professor. “The people in Virginia were campaigning for him not to get a charter. The tactic they used is that [they said], ‘He’s going to use this charter as an excuse to bring Spanish priests and nuns over into Virginia, and they’re going to invade Virginia and take over the colony.’ That argument did prove to be contentious enough that at the last minute, it looked like Calvert was going to lose the territory.”

So there was certainly incentive for Archer, decades before Calvert’s time, to have hidden his Catholicism at Jamestown. “This person could have been from a family that was outwardly Anglican but privately Catholic,” Farrelly said. “That would explain why they would be bringing a relic over with them. It does make you wonder: What was it like for him? How secretive did he feel he needed to be, given that he’s living in a colony that is rabidly anti-Catholic. And who buried him with this relic?”

When archaeologists found the box in Archer’s grave in 2013, they could tell right away that there was something inside. It was light enough to feel hollow, and its contents rattled when researchers turned the box over in their hands.

But they knew as soon as they gently scrubbed off the oxidation from its copper-alloy exterior — a conservation project that took more than 100 hours and revealed a minimalist engraving of the letter “M” — that they wouldn’t be able to open the box without causing irreparable damage. It was through subsequent CT-scan imaging that forensic historians were able to identify shards of bone and the lead ampulla inside, clear evidence of a Catholic relic.

“It was not uncommon — I’m not going to say it was common — but there were two different words to describe somebody who was basically a secret Catholic or a crypto-Catholic in England at the time,” Farrelly told me. “Meaning he attended Anglican church services regularly, and therefore was not subject to fines, but would also attend Catholic services. ‘Schismatic’ was the term that Catholic priests used, and protestants called [them] ‘papists’ … Neither the Catholic priests nor the Anglican priests liked these people. You’re not being true Anglicans and you’re not being true Catholics.”

But there’s still a nagging question in all this: What if the box wasn’t a Catholic relic at all? Such symbols have histories that are, at times, “messy,” Horn acknowledged.

“And this is a line of inquiry we find quite intriguing,” he said. “Perhaps this is a former Catholic holy object that, during the reformation, was translated or repurposed for Anglican use, therefore representing the spiritual heart of the new Church of England in the New World. We know that sacred objects were repurposed for Protestant use, for Anglican use, during this period.”

But there are other hints that suggest Archer was indeed a Catholic, and possibly even an important figure to other Catholics. He was buried in a hexagonal wooden coffin with his head pointing east. “Because of the orientation of archer in the grave, his head to the east, this is usually a sign of clerics,” Horn said. “He could have been the leader of a secret Catholic cell and even possibly a secret Catholic priest.”

Conserved silver reliquary with ‘M’ on lid. (Jamestown Rediscovery Foundation / Preservation Virginia)

Then there are the other Catholic objects, fragments found over the years at Jamestown that are taking on new meaning after the most recent discovery. “We have been finding bits and pieces of rosaries and crucifixes and other things that obviously were Catholic,” Kelso said. “One interpretation is they were bought over here to give to the Indians, even just to trade as trinkets. But now I think about it in a whole different way.”

“A new piece of archeological or historical evidence can help you better understand a whole range of previous evidence,” Horn said. Or, it can call into question much of what you thought you knew.“When you think about the circumstances of Archer’s burial and the way this object was placed — it wasn’t just thrown in surreptitiously,” he said. “It was deliberately placed. It would have been quite public. Someone would have had to get down into the grave. These are real puzzles for us.”

This article appeared in Religion News Service and originally in The Atlantic.