“It was vicious. More than 16 wounds: deep, penetrating cuts, done with real force. Really, it was an atrocious death.”

Edwin Greenwich is sitting quietly, hands slack in his lap, talking about murder.

“We found evidence, too, of wounds that weren’t just simple stabbings, but rather three big lesions to the throat. Two of them would have been lethal. There was also a series of injuries to the cranium, caused by a pitcher of water hurled at him as he was dying.”

The demure anthropologist sits back in his pew, strokes the hair at the nape of his neck.

“In the end, it’s the bones that tell the story. The bones speak.”

Greenwich’s grisly comments sound like a script from a CSI episode. Only in this case, the victim in question isn’t a John Doe recently arrived at the morgue, but one of the most famous figures in South America’s history. The conquistador Francisco Pizarro’s remains may have been entombed here in Lima’s cathedral, where I’m sitting, ever since his assassination in 1541, but that doesn’t mean they’ve been anything near quiet.

Indeed, “quiet” would be the last word to describe Peru’s conqueror. To hear Greenwich, who’s the Director of Bio-Anthropological Research at the cathedral and a resident archaeologist for Peru’s Ministry of Tourism, tell it, investigating the circumstances of Pizarro’s death, as well as his posthumous fate, has been every bit as dramatic as his life.

The story of those investigations reads like a Gothic novel. Missing bodies, hidden underground vaults, a case of mistaken identity, lead caskets full of bones: the 30-year attempt to identify the remains in the cathedral’s front-entryway mausoleum, and how they got there, is full of twists and turns, involving two teams of international experts, myriad scholarly squabbles, and the recent discovery of still more tombs below the cathedral’s floor.

But Greenwich, working hand in hand with one of Pizarro’s lineal descendants, is confident that today we’re on track to know the deathly truth about Peru’s first ruler—and of a host of nameless early limeños that were his contemporaries.

All of which means, my visit to Lima’s 450-year-old cathedral is deathly interesting for me, as I seek to penetrate the country’s fascinating, ferocious history.

“Learning about all this has been like watching a movie,” says the 37-year-old forensic scientist, gesturing toward a stairwell leading down into the cathedral’s crypt.

“Really, it’s made me tense, full of fear.”

Death at Noon

Eleven a.m. Sunshine. Lima’s plaza de armas, where I’ve momentarily stepped out, is a picture of tranquility. Palm-tree shadows flutter on the ornate grillwork balconies. A horse-drawn carriage clops lazily along.

The same hour, however, on June 26, 1541, was very different. On that day, the plaza’s Palacio del Gobierno was the scene of a massacre, as 12 men shouting, “Long live the king!” and “Death to the traitor!” crossed in front of the cathedral to cut down Francisco Pizarro.

They’d been put up to it by Diego de Almagro, Jr. And understandably, since the 19-year-old mestizo youth was out to avenge the death of his father, executed by the great conquistador in Cuzco’s main square three years before.

Diego de Almagro, Sr., had been one of Pizarro’s partners, leading a two-year expedition down to Chile in 1535. But when he failed to discover riches equal to those of the Inca capital—which, to his outrage, he’d been barred from sharing, thanks to Pizarro’s greed and a decree from King Carlos V—he led a mutiny to seize Cuzco from his rivals in 1537.

It failed. Almagro and his co-conspirators were executed in Cuzco’s plaza de armas in July of the following year, thus opening a rift in the Spanish ranks that would ultimately have fatal consequences. The first victim was Pizarro himself. On a Sunday morning in June 1541, the grizzled 63-year-old warrior would be cut down by assassins while having lunch in his palace, just before noon. He was quietly buried in Lima’s cathedral not long after.

Pizarro’s life may have been over. But his posthumous existence was just beginning.

Two Inquests

Edwin Greenwich is standing next to Pizarro’s tomb. It’s an imposing block, all couching lions and mourning angels. Hippogriffs flank the sides, carved in black marble. But Greenwich is focusing on a detail that’s much less grandiose.

“This lead box,” he says, pointing at a glass case, “was discovered in 1977. By accident, really. They were doing restoration work in the crypt, knocking down walls, moving around some other remains. And it was found in the central niche.

“When they examined the box, they discovered an inscription. It said: ‘Here is the head of the Marquis Don Francisco Pizarro, who discovered the new kingdoms of Peru.’ And inside there was a skull, with a jawbone and a sword’s hilt.”

The anthropologist buries his hands deeper into his pockets.

“As you can imagine, it was quite a find.”

Indeed it was—principally because it turned everything scientists thought they knew about the conquistador’s remains on its head.

After Pizarro’s death, his body was interred beneath what is today the Patio of the Orange Trees, on the cathedral’s left side. But subsequent earthquakes, with their attendant reconstructions, caused the cadaver to be moved several times. In 1661, it was finally placed in the crypt below the main altar, where it lay for centuries.

Then, in 1891, Lima’s mayor did something to stir the pot. Wanting to pay tribute to the city’s founder on the 350^th anniversary of his death, he ordered Pizarro’s body to be exhumed and exhibited in a glass case in the cathedral’s front chapel. When the digging commenced, however, what the workmen discovered was a figure that was mummified, like parchment.

Skeptics wondered: why the lack of decomposition? But the remains went to the glass coffin, where they were venerated by limeños for generations.

Until 1977. In that year, the lead box was discovered, creating a scandal in Peru’s scientific community. Was it possible the city had honored the wrong man? Had South America’s greatest conquistador really gone missing for a century, and only recently resurfaced? The powers that be promptly assembled an international team of historians, archaeologists, and forensic scientists to answer the question on everyone’s lips: Were the remains Pizarro’s or not? Led by the archaeologist Hugo Ludeña and the former Minister of Health Uriel García Cáceres, the group worked seven years to establish the truth of the newly disinterred bones.

In 1985, a verdict was reached. The lead box did indeed contain the earthly remnants of the conquistador, fractured cranium and all. Cause of death: severing of the carotid artery.

Even then, though, the controversy continued.

The skull, for starters, didn’t align correctly with the vertebrae. There were fly larvae in some of the joints, contradicting some contemporary chronicles. The jaws failed to match up. Peru’s authorities wanted to lay the remains to rest—literally. But the skeptics were still skeptical.

Enter Greenwich. In 2007, he and a team of youthfully brash investigators proposed, as part of a senior thesis project at Peru’s prestigious San Marcos University, to redo the whole analysis from scratch. In putting forward their project, they went straight to the top: the Archbishop of Lima. To their surprise, His Excellency put them in touch with Hernando Orellana Pizarro, the conquistador’s 17^th great-grand-nephew, who agreed to fund the study through his Obra Pia, an organization dedicated to recovering historic sites from colonial Peru.

The result?

“We found there’s a 90 percent chance the remains are authentic,” says Greenwich. “In police cases, Peruvian law requires only 80 percent for a positive ID.”

It was, the team found, a Julius Caesar-style assassination. Analyzing the bones allowed them to flesh out what happened with additional (gruesome) details. One assailant had tried to chop Pizarro’s head off from behind. Another nearly cut out his left eye.

And the mummy exhibited in the glass case? The conquistador’s stand-in while he went missing?

“We still don’t know who that was,” Greenwich shrugs.

Into the Vault

I’m crouching on a narrow underground catwalk, one that leads to a deep stone well. I have to duck to keep from bumping my head. Around me, shallow pits of bones, eerily lit by floodlamps.

“We discovered this in the course of our diggings,” Greenwich explains. “One hundred eighty people were buried here, many of them children. In one grave, we found a mother, with a newborn in her arms.

“Really, it’s like a cross-section of colonial Lima.”

Where we are is under the shrine of the Virgen de la Candelaria, in the cathedral’s back right corner. Previously, the church was considered to have only a single crypt, where viceroys, archbishops, and other powerful figures were laid for their final rest. But in 2011, hot on the heels of the Pizarro investigation, Greenwich and his colleagues stumbled onto two mass tombs, shedding new light on the posthumous destinies of ordinary Josés and Marías in viceregal Peru.

“We’ve learned so much about everyday limeños. One of these gravesites was for a shoemaker’s guild. The people were buried in layers, with lime between to prevent the odors of decomposition. These people were of a slightly higher standing.”

He pats a side wall with his palm.

“Meanwhile, in the other grave, the bodies were all jumbled together. These were people from all walks of society. Criollos [locally born whites], mestizos, even blacks.”

What Greenwich uncovered was not altogether surprising. Before the construction of Lima’s first public cemetery in 1808, colonial limeños were in the practice of interring their dead below the churches—most famously, in the Iglesia de San Francisco just around the corner, which attracts countless visitors with its eerie catacombs. But now, it turned out, Lima’s cathedral, too, had its macabre substructure.

Was it possible the cathedral had other subterranean tombs, ones that awaited the right investigator?

“Very possible,” Greenwich says. “We just don’t know.”

The anthropologist and I walk out of the cathedral’s gloom, into the bright sunlight of the plaza.

I ask what other forensic projects he’s got in the pipeline, now that he’s dug out the innards of Peru’s principal church.

“Bueno, right now we’re working on an exploration of some caves of Intimachay, in Peru’s Amazonas region. I’m excited.”

He crosses his arms, looks out on the square.

“But Lima will always fascinate me. It’s a place you can study forever, really. It’s full of mysteries.”