MALVERN, Pa. » They laid his bones in a bed of Bubble Wrap, with a care beyond what is normally given to fragile things. They double-boxed those bones and carried them last month to the United Parcel Service office on Spruce Street in Philadelphia. Then they printed out the address and paid the fee.

With that, the remains of a young man were soon soaring over the Atlantic Ocean he had crossed once in a three-masted ship. His name is believed to have been John Ruddy, and he was being returned to the Ireland he had left as a strapping teenage laborer. In 1832.

His voyage home is the latest turn in the tale of Duffy’s Cut, a wooded patch that is little more than a sylvan blur to those aboard commuter trains rocketing past. It is a mass grave, in fact: the uneasy resting place for dozens of Irish immigrants who died during a cholera epidemic, just weeks after coming to America, as an old song says, to work upon the railway.

For the last decade, a different kind of rail gang — professors and students, scientists and landscapers — has been digging away at the layers of soil, myth and silence to unearth the unlucky inhabitants of Duffy’s Cut and place them in both historical context and consecrated soil.

"The first seven bodies were here," said Bill Watson, 50, pointing to a brown-gray swath of muck as a downpour battered the dead leaves and another train whined past. A history professor at Immaculata University in Malvern, he is also the de facto foreman of this erudite rail gang.

"And this is the shanty," Watson said, rainwater pouring off the brim of his baseball cap. "This is where the men lived."

It begins in late June 1832, when the John Stamp docked in Philadelphia, ending a two-month sail from Derry in northern Ireland. On board were dozens of young Irishmen eager to begin their American climb, bearing the names of Devine, and McIlheaney, and Skelton — and Ruddy, at 18 the youngest.

Working for a contractor named Duffy, a crew of about 120 men was soon digging through clay and shale to fill the lows and level the highs for a train line. "A sturdy-looking band of the sons of Erin," a local newspaper called them.

But an outbreak of cholera caused a Philadelphia panic that hot summer. The disease struck the work site, probably by way of a contaminated creek running past the men’s crude living quarters — their shanty. The local community shunned the sick foreigners, leaving acts of kindness to a few courageous Sisters of Charity who ventured out from Philadelphia.

When the epidemic subsided, the official account of the sad but unremarkable toll at Track Mile 59, also known as Duffy’s Cut, was eight dead, with the shanty burned down and buried by a humane blacksmith. Life continued along its track. Almost immediately, though, there came folkloric whispers of something not right. Glowing apparitions were said to have been seen dancing down at the cut.

An Irish railroad worker eventually fenced off a spot in the general area, out of respect. Then, in 1909, a midlevel rail official named Martin Clement erected a granite-block enclosure. But his superiors said no to an explanatory plaque, a decision that left generations of hikers to encounter a memorial without context in the middle of the woods.

Nearly a century passed before serendipity finally blessed Duffy’s Cut.

Watson and his twin, Frank, a Lutheran minister, were sorting through family things in 2002 when they took a close look at an old file. It turned out that this Martin Clement, who later became president of the Pennsylvania Railroad, had kept an extensive file on Duffy’s Cut, and that his executive assistant — their grandfather! — had taken the file after the railroad vanished into a merger in the late 1960s.

These internal records indicated that at least 57 people — not eight — had died at Duffy’s Cut. "Something was off," Bill Watson said. "It made us dig deeper."

Working closely with a handful of passionate colleagues, the Watsons did extensive historical research before creating a rough grid of the site. On a hot August morning in 2004, they began their dig with the help of a few college students, all young men of the same age as those who had come with shovels to these woods nearly 170 years before.

For months, nothing. Then a pot lid. Then, in November 2005, Bill Watson uncovered the bowl of a clay pipe — the requisite prop for a 19th-century Irish stereotype — adorned with shamrocks and a small harp. Symbols of Ireland.

"That for us was the holy grail," Watson said. "It meant this wasn’t just an urban myth."

The hunt-and-peck excavation intensified when the team enlisted the help of Tim Bechtel, a geophysicist. Using ground-penetrating radar and electrical imaging, he scanned the site the way a radiologist would a body, and directed the team to what he called the "anomalies."

In March 2009, two students found a tibia, then more. Before long, skull fragments and other remains were laid on a table in a conference room at Immaculata, beneath a crucifix, for an examination by Janet Monge, a physical anthropologist and the curator at the University of Pennsylvania Museum, and Dr. Matt Patterson, a local dentist with training in forensic odontology.

A muscular man in his late teens, they concluded, who had never developed an upper right first molar — a dental variance that Patterson called "exceptionally rare." The skull also had evidence of blunt-force trauma, Monge said. "He got wonked on the head."

The discovery prompted more research and more digging. Over the next two years, six more sets of remains were located, although one had been reduced by the acidic Pennsylvania soil to little more than a stain. Here, for example, was a man beneath a tulip poplar. Another man, nicknamed "the tall guy." And a woman, who had probably been hired on as a laundress and cook.

The team also uncovered iron forks and pottery shards, handmade glass buttons and pieces of other clay pipes — and coffin nails. Here was evidence of a shanty community and the burial of caskets, far from any church cemetery.

Monge found signs of blunt head trauma in three more sets of remains, as well as a bullet hole in another. For the researchers, these forensic clues, coupled with contemporaneous news accounts, conjure a possible sequence of events in which a few workers escaped from an enforced quarantine, were subdued and killed, then returned in coffins to Duffy’s Cut, where the rest soon died of disease. Then all were buried in an anonymous grave.

"I actually think it was a massacre," Monge said.

A year ago this month, the remains of four Irishmen and one Irishwoman, 180 years dead, were buried beneath a limestone Celtic cross in a cemetery just outside Philadelphia. The search for their shantytown comrades continues; Bechtel has already found a "very concentrated anomaly," 30 feet deep, that the team hopes to excavate sometime this year.

Meanwhile, research by Patterson and Monge found that some Ruddys in County Donegal are known to have a certain dental variance: the absence of an upper right first molar. That fact, coupled with the passenger list from the John Stamp, prompted the decision by the research team to ship back to Ireland the remains of the first victim they had found.

Three weeks ago, the Watson brothers joined a small crowd gathered in a church cemetery in the small Donegal town of Ardara. They prayed and sang under a limestone sky, as a young laborer, late of Duffy’s Cut, received his delayed but proper burial.

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