MEXICO CITY >> The skeleton is that of a young woman, perhaps an Aztec noble, found intact and buried in the empire’s most sacred spot more than 500 years ago. Almost 2,000 human bones were heaped around her, and she is a mystery.

There are other discoveries yet to be deciphered from the latest excavation site at the heart of this vast metropolis, where the Aztecs built their great temple and the Spanish conquerors laid the foundation of their new empire.

Before announcing the discovery of the unusual burial site and the remains of what may be a sacred tree last month, archaeologists had also recently found a giant round stuccoed platform decorated with serpents’ heads and a floor carved in relief that appears to show a holy war.

Mexico City might be one of the world’s classic megacities, an ever-expanding jumble of traffic, commerce, grand public spaces, leafy suburbs and cramped slums. But it is also an archaeological wonder, and more than three decades after a chance discovery set off a systematic exploration of the Aztecs’ ceremonial spaces, surprises are still being uncovered in the city’s superimposed layers.

“It’s a living city that has been transforming since the pre-Hispanic epoch,” said RaC:l Barrera, who leads the exploration of the city’s center for the National Institute of Anthropology and History here.

“The Mexicas themselves dismantled their temples,” to build over them, he explained, using the Aztecs’ name for themselves. “The Spanish constructed the cathedral, their houses, with the same stones from the pre-Hispanic temples. What we have found are the remains of that whole process.”

Perhaps nowhere else in the world is the evidence of a rupture between civilizations as dramatic as in Mexico City’s giant central square, known as the Zocalo, where the ruin of the Aztecs’ Templo Mayor abuts the ponderous cathedral the Spanish erected to declare their spiritual dominance on the conquered.

“I think the ideological war was more difficult for the Spanish than armed warfare,” said Eduardo Matos Moctezuma, the archaeologist who first led the excavation of the Templo Mayor.

There are other, older places in the world where ruins rise from traffic-clogged streets, where foreign invaders ended empires. But it is different here, academics say.

“They blew the top of it off; they didn’t do that to the Coliseum,” said David L. Carrasco, a historian of religions at Harvard University who has written on the Aztecs and the excavations at the Templo Mayor. “In Rome, the ancient Roman city stands alongside the medieval and the modern city.”

A Spanish chronicler of the conquest, Bernal Diaz del Castillo, wrote that “of all these wonders” of the Aztec capital, Tenochtitlan, “all is overthrown and lost, nothing left standing.”

Since 1790, though, when construction work to pave the Zocalo unearthed the first giant Aztec carvings, Tenochtitlan has been giving up its secrets. Archaeologists began exploring the Templo Mayor a century ago, but the discovery of a giant monolith depicting the decapitated, dismembered Aztec moon goddess Coyolxauhqui in 1978 led to a full-scale excavation that continues today.

In the first five years, archaeologists had uncovered large parts of the temple that lay underneath a structure razed by the Spanish after the 1521 conquest. Past Aztec emperors had built new temples over earlier ones, which unwittingly spared the older structures.

The archaeological project “wasn’t just that we were going to find an enormous temple,” Matos said. “It was what it meant within Aztec society. That building was very important because for them it was the center of the universe.”

There is still much more to uncover around the Templo Mayor. The 16th century Franciscan Friar Bernardino de Sahagun left a record of what Matos calls the Aztecs’ sacred precinct of temples and palaces, now a densely packed square about seven blocks on each side.

The Sahagun account, compiled from Aztecs’ recollections of their lost city, has proved strikingly accurate. Of the 78 structures he described, archaeologists have found vestiges of more than half.

During the most recent excavation, underneath a small plaza wedged between the Templo Mayor and the cathedral, Barrera had been looking for the round ceremonial platform because it had been described in the Sahagun record.

Much of what the friar and other witnesses chronicled now lies as deep as 25 feet underground. To get there, Barrera’s team must first navigate the electricity lines and water mains that are the guts of the modern city and then travel down through a colonial layer, which yields its own set of artifacts.

“It is like a book that we are trying to read from the surface to the deepest point,” he said.

But despite the guidance from historical records, Mexico City’s archaeologists cannot dig anywhere they please.

Part of the sacred precinct is now a raucous medley of the mundane. The street vendors hawking pirated Chinese-made toys and English-language lesson CDs from crumbling facades are merely the loudest. To excavate under the area’s hotels, diners, cheap clothing stands and used bookstores would entail fraught negotiation.

Along the quieter blocks of the precinct, handsome colonial structures are now museums and government buildings, themselves historical landmarks.

Archaeologists believe that the Calmecac, a school for Aztec nobles, extends under the courtyards of Mexico’s Education Ministry building. For now, the only part of the Calmecac that has been excavated are several walls and sculptures on display under a building housing the Spanish cultural center, discovered when it was remodeled.

Still, in a strange sort of payback, the ruins themselves sometimes make it possible for the archaeologists to enter private property and begin digging.

Since the 16th century, the city has pumped water from deep wells to satisfy its thirst, causing the clays beneath the surface to sink as water is sucked from them, rather like a dry sponge.

But the buildings settle unevenly, buckling over the solid stone Aztec ruins below, lending many of the sacred precinct’s streets a swaying, drunken air.

As cracks open and the buildings tilt, many of them need restoration, which by law allows archaeologists from the anthropology and history institute to keep watch. If historic remains are found, the owner must foot the bill to restore them.

When the cathedral needed to be rescued in the 1990s, engineers dug 30 shafts to stabilize the structure and Matos and his team descended as far as 65 feet to see what was underneath.

“It’s the vengeance of the gods,” he said. “The cathedral is falling and the monuments to the ancient gods are what’s causing it to fall.”

Among other things, the archaeologists found the remains of Tenochtitlan’s ball court, where Aztecs played a ritual ballgame common across ancient Mesoamerica. It remains sealed deep under the cathedral’s apse and the cobblestone street to its north.

“That whole part of the city is like a graveyard of people and of significant cultural objects,” Carrasco said. “And they awaken every time Mexico reaches for its future.”

© 2012 The New York Times Company