Squatting in a pit dug for the dead, local worker Felix Mejia exposes the tops of two Inca skulls. Also visible is a piece of copper and two spondylus shells, valuable artifacts suggesting that those buried here were of high rank.

In a sprawling shantytown called Tupac Amaru on the outskirts of Lima, children play in the dust of ages. Beneath their feet, preserved by the bone-dry soil, lies one of the largest Inca cemeteries yet found in Peru. This pre-Hispanic site, known to archaeologists as Puruchuco-Huaquerones, dates from the Late Horizon (1438 to 1532). Though it has been designated a national monument, my team of scientists has had to race against development to pull the past out from under the burgeoning present. Beneath the schoolyard alone, one of 15 areas examined in three years, we've salvaged more than 120 mummy bundles (layers of cloth encasing a body and personal effects) typical of pre-Inca and Inca burials.

The story of how Tupac Amaru came to be is a common one in Peru. In 1989 some 340 families fleeing guerrilla activity in the highlands settled on this property, misled by land traffickers to believe they would soon be given title. Meanwhile, six feet (two meters) under and defenseless against the sudden influx of sewage and water, the mummies were decomposing. Some squatters dug them up and burned them, hoping to avoid a scientific excavation that would delay town development.

Though much damage was done in subsequent years, the Peruvian Institute of Culture (INC) finally did request an archaeological evaluation of the area. I arrived from Lima in 1999, tools and team in tow. Not wanting to be relocated by the government, the townspeople—then more than 1,240 families—agreed to stop leveling the land and even scraped together money to help fund our work. They hoped it would be a long-term investment, encouraging the government to give them what the traffickers couldn't: clear land titles and basic utilities.

At first the residents assumed we would loot the tombs or dig briefly and halfheartedly, pocketing leftover funds. But we hired locals to help excavate, soon earning their trust. In addition, the INC visited the site weekly. In three field seasons we've removed, examined, and photographed more than 2,200 individuals of all ages and ranks buried within 75 years of one another. At 20 acres this is the second largest cemetery ever excavated in Peru (after Ancón) and the largest from a single time period. A local museum will ultimately display these cultural treasures.

As we continue to delve into the past, life in Tupac Amaru flourishes. Children frolic on sacred ground, running along the rims of our excavations, peering into the tomb of a dead man who has claimed their soccer ball. Some believe the spirits of the deceased have caused a spate of illnesses here, including my own lingering cough. Indeed, inhaling dust of the dead can lead to bacterial infection. Yet many say they are not fearful but elated by their privileged view of those who walked this land before them.