BERLIN.- From under a parking lot in the center of Berlin, a team of archaeologists unearthed ancient human skeletons of nearly 4,000 forgotten dead from a bygone church cemetery paved over by a former communist regime.

That was nearly two decades ago. In that time, scientists plumbed information from inside bones — some older than 1160 — and in between ancient teeth. They made startling discoveries, including that the city was inhabited nearly a century earlier than believed.

But bones hold only so many secrets. With much of the research on these earliest Berliners complete, the remains of 100 medieval and early modern babies, children and adults have now been returned to the heart of the city. They will rest in state in a museum, Petri Berlin, at the same place where they had been ignominiously blacktopped over.

And so, on a Saturday last month, in an act of repentance and reverence dreamed up by the project’s lead archaeologist, a horse-drawn hearse and 100 present-day Berliners carried the coffins of the early settlers through the streets of the city in a grand funeral.

“I thought, ‘We have found the graves of almost 4,000 people, and I wanted to show how much life that is,’” said Claudia M. Melisch, the lead archaeologist who oversaw the excavation of the former cemetery of St. Peter’s Church, where the bodies had been buried, long before the church was torn down in 1964. “It is a gesture from us recognizing their existence.”

The funeral procession began in the 17th-century crypt beneath the Parochial Church, a different church in the Mitte neighborhood of Berlin. There, arranged in neat rows in the dimly lit arched corridors beneath the church were 30 miniature wooden coffins. Each contained the remains of a baby. Another 70 more small boxes held adult bones, every last one topped with a calla lily and sprigs of wildflowers.

The volunteers acted as pallbearers. Some were from the archaeological community and others were Berliners who had followed the project in news reports. One by one, they descended into the crypt to collect the coffins, all of which contained letters that Melisch had written with the biographical details scientists gleaned from the bones of each occupant.

A curled spine revealed a person wracked by tetanus, one of the letters explained, an opening in a tiny skull likely a congenital defect of a baby who died in the 1300s at birth.

On her lap in her wheelchair, Brygida Mrosko, 71, carried a funeral wreath. A retired lawyer, Mrosko had read about the event and felt compelled to pay her respects to her fellow Berliners whose relatives had been lost to time. “This is their last voyage as Berliners,” Mrosko said. “It’s our duty to make it with them.”

The march began with prayers by both the protestant clergy of the Parochial Church, but also a Catholic blessing. Many of the dead were born before the Protestant Reformation in the 1500s, Melisch realized, so she had invited representatives from the Archdiocese of Berlin to make sure these dead, too, were blessed in accordance with their faith.

Dressed in his ceremonial chasuble and zucchetto cap, Gregor Klapczynski, a Catholic Church historian from the Archdiocese, swung a thurible of frankincense to bless the proceedings.

The scientific study of the bones, which included sawing pieces off for radiocarbon dating and grinding up teeth to study hidden isotopes that would reveal information on the food they ate, did not desecrate the bodies, he said. It honored them. “In the Catholic opinion faith and reason are very connected,” Klapczynski said as perfumed smoke rose around him.

The excavation began in 2007 to make way for a new multifaith center called the House of One, which will be built on the site and house a church, a mosque and a synagogue. The original house of worship there had been first established around the year 1150, Melisch said. Its final iteration appeared to be damaged during World War II by the Soviet army, and ultimately razed by the communist government that controlled what was then East Berlin in the 1960s.

The dig, which took three years, revealed the buried foundation of an ancient church and other buildings, as well as 3,221 graves. Some were stacked upon one another in an overstuffed churchyard, and contained the bodies of 3,778 people.

Melisch, who had worked on excavations in Greece and Pompeii, Italy, recruited an international group of colleagues — osteologists, geneticists and bioarchaelogists — from past digs to the project, some of whom, like her, volunteered much of their time to mining the bones for information, she said.

“Normally we excavate an area, we clean its monuments and then we leave,” Melisch said. But the sheer volume of bodies discovered, and her own personal connection to the city, made the project at Petriplatz, or St. Peter’s Place, feel different. “Here I felt I have this responsibility with it,” she said, her eyes welling. “Each individual is like the chapter of a book, which has not been read.”

As the hearse wagon set out Saturday morning from the churchyard, with a driver in a top hat steering its two Belgian draft horses, the volunteers filed behind solemnly. They marched in silence down Gertraudenstrasse, or St. Gertrude’s Street, where Melisch said historical records indicate many more bodies still lie beneath the asphalt.

Hugging a tiny coffin to her chest, Marla Hujic, a 6-year-old, walked beside her mother, Alisa. “I’m burying a child,” Marla said.

Carrying the remains of a 700-year-old toddler, Michael-Josef Richter, 60, an author, said he was struck by a sense of connection to the people who had come to this city before him. “These people lived and loved here for the same reasons that I came to Berlin for,” Richter said.

The haunting tones of a gong sounded over the marchers and the coffins. It was played by a musician, Peter Schindler, 64, who had decided to bring the East Asian instrument.

“They were the very first Berliners, and when you live in this city you have to say thank you to them for establishing this city,” Schindler said. “It is the place I found dreams I never had before.”

At the Petri, the mourners filed into an exhibition space where the old stones of the original church were visible. There, they handed some the tiny coffins and boxes to Melisch and Matthias Wemhoff, the director of the Museum of Prehistory and Early History, who slid them into the shelves of the ossuary. From her wheelchair, Mrosko laid the wreath she had borne on what would have once been the ancient church’s floor.

“Our very last voyage is to God in heaven,” Mrosko said earlier as she helped the bones on their journey. “This is their penultimate voyage.”

This article originally appeared in The New York Times.