It's a mystery that has intrigued Americans for centuries: What happened to the lost colonists of North Carolina's Roanoke Island? (See "America's Lost Colony.")

The settlers, who arrived in 1587, disappeared in 1590, leaving behind only two clues: the words "Croatoan" carved into a fort's gatepost and "Cro" etched into a tree.

Theories about the disappearance have ranged from an annihilating disease to a violent rampage by local Native American tribes. Previous digs have turned up some information and artifacts from the original colonists but very little about what happened to them.

Until now.

View Images MAGGIE SMITH, NG STAFF. SOURCE: FIRST COLONY FOUNDATION Illustration by North Wind Picture Archives/Alamy

Thanks to technological advances and a cover-up on a map, researchers are getting closer to finding out what happened to the lost colony of Roanoke Island.

What Do We Know?

The lost colonists were the third group of English arrivals on North Carolina’s Roanoke Island, settling near the modern-day town of Manteo.

The first group to arrive, in 1584, came to explore and map the land for future groups. A second group, which arrived in 1585, was charged with a military and scientific mission. But this second group's trip was far from peaceful.

"That's where tensions begin [with the local Native American tribes]," said Clay Swindell of the Museum of the Albemarle in Elizabeth City, North Carolina, a member of the archaeology team investigating the colony. He says that this second group was driven out in 1586 by local tribes angry that the colonists were taking up good land and resources.

The third group arrived in 1587. Entire families came with children—17 women and 11 children accompanied a party of 90 men. That meant the group wanted to settle in the New World and was not a military excursion, which would have included only male explorers.

A Map With Secrets

A clue uncovered in a long-forgotten, centuries-old map of the area called "La Virginea Pars"—drawn by the colony's governor John White—kicked off a reexamination of the fate of the lost colonists. An artist and employee of explorer Sir Walter Raleigh, White was later appointed governor of the new lands; he was also the grandfather of Virginia Dare, the first English child born in the New World.

Two patches on the map made Brent Lane of the First Colony Foundation (the group behind the latest archaeological trip and whose work is supported by National Geographic and the Waitt Grants Programs) in Durham, North Carolina, wonder if they might hide something beneath.

Scientists at the British Museum looked into the patches and discovered a tiny red-and-blue symbol. Could it have indicated a fort or a secret emergency location?

"Our best idea is that parts of Raleigh's exploration in North America were a state secret, and the map 'cover-up' was an effort to keep information from the public and from foreign agents," said Eric Klingelhofer of Mercer University in Macon, Georgia, a historian and the principal investigator on the project.

Disappearing Act

Most researchers think the colonists likely encountered disease—caused by New World microbes their bodies had never encountered before—or violence.

The research team thinks that when the crisis—whatever that may have been—hit, the colonists split up into smaller groups and dispersed.

"It's a good strategy," he said, explaining that the previous group from 1585 had been ordered to do so if disaster struck. "We don't definitely know that they do, but it's obvious that that's the only way they could have survived. No single Indian tribe or village could have supported them. They would be even larger than some villages—I mean, they were over a hundred people."

The prevailing theory has been that the colonists abandoned Roanoke and traveled 50 miles south to Hatteras Island, which was then known as Croatoan Island. But, Klingelhofer said, what if they went in another direction?

What if some of the colonists traveled west via Albemarle Sound to the mouth of the Chowan River, to a protected inlet occupied by a sympathetic tribe? (See "What 'Sleepy Hollow' Didn't Tell Us About Roanoke's Lost Colony.")

Furthermore, archaeologists have identified the nearby site of a small Native American town named Mettaquem, which may have adopted some of the colonists. Klingelhofer said that while researchers don't know much about the Native American town and its inhabitants, its existence has been verified.

"It's a very strategic place, right at the end of Albemarle Sound," he said. "You can go north up the Chowan River to Virginia or west to the Blue Ridge Mountains. They were big trading partners" with other Native American tribes.

After the map's secret was revealed, Klingelhofer, along with the First Colony Foundation, which studies the first attempts at colonization in the New World, proposed a return trip to the area, with a twist. This time, shovels would have 21st-century helpers—magnetometers and ground-penetrating radar (GPR).

Using Modern Technology

Malcolm LeCompte, a research associate at Elizabeth City State University in North Carolina, was responsible for the addition of GPR in the archaeological search for what happened to the lost colonists of Roanoke.

The process began earlier this year with a satellite survey of the site.

"What we do is we get the oldest maps we can find—so we can get a historic sense of what was there and what's there now—and orient them," LeCompte said. The point is to compare "what may have been there in the past to what is there now."

Researchers look for similarities between the old maps and the current geography of the area. Once they identify where the spots on the map correspond with today's landscape, a painstaking process of laying out a grid and systematically searching it with their GPR ensues.

The technology emits radio waves into the ground and measures the echo as the signal bounces off of various things buried underground. Essentially, it measures the depth that signals travel before hitting something that causes a measurable bounce back. In other words, signals potentially indicate a hidden object underground.

Metal objects—like the iron cannons that have been found at the site—act like "giant antennas." Graves and coffins are also detectable, because they contain voids with different densities and poorer conductive properties than the surrounding soil.

LeCompte and his colleagues found a previously undetected pattern that may indicate the presence of one or more structures, possibly made of wood, under about three feet (a meter) of soil.

"I don't know if it's one or a group [of structures]," he said, adding that they "could be joined or they could be close together." Perhaps the wood of the structures collapsed over time, leaving impressions in the surrounding soil, LeCompte speculated.

The Museum of the Albemarle's Swindell suggested the use of a proton magnetometer to enable the researchers to double-check their GPR findings. Much more sensitive than a metal detector, the device can spot objects buried about 13 feet (four meters) underground.

The device measures distortions of the Earth's magnetic field due to the presence of various objects buried underground.

"We're looking for anything that affects the local magnetic field," Swindell stressed. "That could be things like burn pits."

Swindell, for his part, thinks there may also be remains of a palisades that would have been used by farmers to keep wild animals away from crops.

The presence of the buried structure and the fence strongly indicate that there was some sort of colonial presence in the area. What complicates the story further is the presence of later colonial sites in the area through the 1700s.

Unfortunately, neither piece of technology has shed light on the role of Native American populations in the area. That's a puzzle that remains to be solved.

It's Complicated

In the days of the Roanoke Colony, relations with the local Native Americans were mixed.

Roanoke was geographically located in the crux of sociopolitical friction between the Secotan—who held sway over Roanoke—and the Chowanoke, who controlled the nearby waterways.

Tensions were especially high between the colonists and the Secotan tribe.

"There is no doubt that there was a lot of hostility," Klingelhofer said. "Not all the tribes were hostile, but some of them were hostile. They felt imposed upon. There was fighting between [the groups]"—both among the tribes, and between some of the native peoples and the English settlers.

It didn't help that the English attempted to explore the area multiple times. The group that arrived prior to the lost colonists were driven back to England, which meant when the ill-fated third group of colonists showed up, some sour feelings remained.

"It would not surprise me that the Secotan would want to be done and get rid of the English," Swindell said.

Whether groups of Secotan banded together to rid themselves of what they saw as interlopers is anyone's guess, he said.

The area does seem to hold clues to contact between local tribes and European colonists in the 16th and 17th centuries.

The next step in solving this age-old American mystery? "We have to go in and dig some holes, I guess," Swindell said.