NORFOLK, Virginia — No one knows how many skeletons are under St. Mary’s in Norfolk, or why the 162-year-old Catholic church was built right on top of a cemetery.

But when David Givens, Jamestown’s head archaeologist, recently rolled a ground penetrating radar over the sanctuary’s concrete floor, he detected void after void.

Graves, he said, “are everywhere under here.”

Church legend has long whispered of such things.

Confirmation came last fall when contractors removed part of the floor to install sewer lines for new bathrooms and found the faint borders of a brick crypt.

Then a skull — or at least part of one — turned up in a utility hole cut near the altar.

Renovations screeched to a halt.

Now, the congregation of the Basilica of St. Mary of the Immaculate Conception just wants to know who’s under there.

The church, one of the oldest among its faith in the commonwealth, has always been unusual — a vaulted, stained-glass, Gothic-inspired work of architecture listed on state and national historic registries.

It’s one of just two Catholic churches in the state designated by the pope as a “minor basilica” — a place of special pilgrimage — and the only one in the country with a predominately African American flock.

A holy place. Consecrated. Steeped in spirit and soul.

Above ground.

And apparently below.

What happened all those years ago at St. Mary’s would be highly illegal today. A felony.

Even more of a mindboggler: The dead under the floor are assumed to be the church’s very own — worshippers from earlier congregations, the kind of ancestors whose remains tend to get more respect.

Their stories start 20 years after the end of the American Revolution, when a small, wooden chapel was built around 1802 on the parcel, a few low-lying acres now brushed by the City Hall exit ramp of I-264.

The chapel — the first formal home for the Catholic faith in the area — served a largely immigrant community: Irish, French, Spanish, escaping tough times, oppression or revolutions in their own countries. Old maps point to a burial ground in a quadrant of the plot.

The chapel evolved into bigger and better buildings until its footprint was occupied by a substantial structure called St. Patrick’s. It was heavily damaged in a fire in 1856 — a suspected arson, punishment for holding interracial services.

By 1858, the parish had renamed itself St. Mary’s, transformed the ruins of St. Patrick’s into a parish hall and built a new house of worship — larger, grander than ever and on a different section of the land, the piece that held its own cemetery.

But while some historic churches, like Williamsburg’s Bruton Parish, do have members interred under their floors, such graves are preserved as places of honor and marked with chiseled slabs.

At St. Mary’s, headstones were removed and the final resting spots of relatives and friends erased — cleaved by foundation or drainage work, entombed and forgotten beneath a soaring sanctuary and gleaming spire.

Why was that considered OK?

Church records from the era are sparse or missing entirely, making “it hard to get inside their heads,” said Father Jim Curran, who leads the current congregation.

Certainly, life in general was harder and shorter back then. And in Norfolk and Portsmouth alone, the 1855 yellow fever epidemic had just claimed 3,000 souls.

“There were so many burials, so much death,” Curran said. “They were not as distant from it as we are. They lived with it every day.”

Maybe cemeteries weren’t viewed in such an untouchable light.

“I just don’t think death had the same ominous feel,” Curran said.

Now though, the discovery of St. Mary’s underworld was enough to hit the brakes on a $6.5 million, multiyear renovation.

The restoration and repair project, which mushroomed from a leaky roof, was already behind schedule and quite complicated, calling for experts in historical architecture to meet standards, accessing tax credits to help cover the cost.

But the graves plunged the congregation into a whole new chapter of legalities, agencies and specialists.

Not to mention a tangle of ethical questions.

Should the entire floor be uprooted — a renovation nightmare — so all remains could go to a proper cemetery? Or should they be left to rest in peace, imperfect as it was?

According to present-day law, graves must be left undisturbed unless a “compelling” application can be made for exhuming and re-interring elsewhere, said Paige Pollard, owner of Commonwealth Preservation Group, hired by the church for guidance.

Construction has been known to qualify. But church members quickly retooled their wishlist, deciding they did not need new bathrooms or any other improvements that badly.

“They didn’t feel like it was appropriate to disturb the graves any more than they already had been,” Pollard said.

At that point, the congregation could’ve simply sealed everything back up. Moved on.

But they were curious, wanting to know more about the people inside the long-hidden graves.

It’s unlikely they’re direct relatives of today’s members. St Mary’s, with 1,000 households on its roll, has been largely African American since the 1960s.

“That didn’t matter to them,” Curran said. “It’s still part of the history of St. Mary’s.”

And given the church’s past penchant for blurring racial lines, “you never know.”

So the jackhammered section of floor was left open and a permit to exhume a handful of graves for study was obtained from the Virginia Department of Historic Resources.

In recent weeks, St. Mary’s has resembled more of an archaeological dig than a church.

“My parishioners, to a person, just really wanted this,” Curran said.

Besides, it’s already been four years since the renovation moved their services into the parish hall.

“What’s another few months?”

Just inside the cool, dim sanctuary, archaeologists probed and puzzled over the secrets of St. Mary’s.

The discovery of a brick tunnel — 4 feet tall, 3½ feet wide — had added to early excitement.

“My imagination went straight to the Underground Railroad,” Curran said, referring to a pre-Civil War network of secret routes used to help slaves escape to the North.

It’s possible the tunnel served as a passage, but its original purpose appears to have been drainage.

Mike Clem, state archaeologist for the region, explored about 40 feet inside the tunnel until it dog-legged into an even narrower one and became so tight he had to army crawl backward to retreat.

He mostly encountered silt, “but I did have a bad dream about it that night,” he said. “I woke up like, ‘What was I thinking?’ “

The tunnel cuts right through graves — some with brick-lined burial chambers, some without. Sections of church foundation or previous renovation work do the same.

“Almost all have been impacted in one way or another,” said David Brown of DATA Investigations, a Gloucester-based research outfit that’s heading up the exhumations. “I wish they hadn’t destroyed as many as they did.”

Five graves were chosen for excavation, a meticulous process requiring hand trowels, bent backs and dirty knees to reach fragile, rusty-colored remains. Wooden coffins and funeral clothing had long since melted away, leaving only traces of hinges and nails, scatters of buttons and pins.

One grave held the remains of two, most likely mother and child.

Another, breached by the tunnel, had a jumble of human bones plus cow and other types of animals — evidence that a rat or some other creature had once used the damaged grave as a den.

One crypt was nearly empty, containing only fingers, toes, kneecaps and a few rib fragments. Brown believes that indicates a sloppy but well-intentioned effort to remove at least some of the dead before the church encapsulated their graves.

“We’d heard stories that congregants were given a chance to exhume family members,” he said. “But I don’t think many did. It would have been expensive.”

Unearthed remains will be transferred to laboratories, where they’ll be read like road maps to long-ago lives. Age. Gender. Diet. Injuries. Illnesses. Isotopes in teeth can even hold clues to the regions where a person has lived.

Molecular anthropologists at the University of Pennsylvania have offered to do DNA testing. In addition to revealing ethnicity, it could make connections to someone living today. But the testing requires an additional permit that’s still in the pipeline. A tiny bit of bone gets destroyed in the process, which requires special permission.

When all has been learned that can be, the remains will be re-interred at a cemetery near the Norfolk zoo, about two miles away. That cemetery, also named St. Mary’s, was purchased by the parish around the time the church was built and holds a smattering of tombstones that seem linked to the old days.

The new arrivals will be buried with dignity and marked with fitting memorials.

For those left behind, Jamestown’s GPR will provide a map of their locations so the church can ensure they’re not ruffled again.

They’ll sleep under the floor forever.

Clem, from the department of historic resources, thinks the occupants of those graves might not object.

Even concealed, their spots seem suitably sacred.

“To have this elaborate cathedral on top of you? That doesn’t sound so bad to me.”