On the remote Peruvian island of Taquile, in the middle of the great Lake Titicaca, hundreds of people stand in silence on the plaza as a local Roman Catholic priest recites a prayer. Descended in part from Inca colonists sent here more than 500 years ago, the inhabitants of South America's Taquile keep the old ways. They weave brilliantly colored cloth, speak the traditional language of the Inca, and tend their fields as they have for centuries. On festival days they gather in the plaza to dance to the sound of wooden pipes and drums.

Today, on a fine summer afternoon, I watch from the sidelines as they celebrate the fiesta of Santiago, or St. James. In Inca times this would have been the festival of Illapa, the Inca god of lightning. As the prayers draw to a close, four men dressed in black raise a rustic wooden litter holding a painted statue of Santiago. Walking behind the priest in a small procession, the bearers carry the saint for all in the plaza to see, just as the Inca once shouldered the mummies of their revered kings.

The names of those Inca rulers still resonate with power and ambition centuries after their demise: Viracocha Inca (meaning Creator God Ruler), Huascar Inca (Golden Chain Ruler), and Pachacutec Inca Yupanqui (He Who Remakes the World). And remake the world they did. Rising from obscurity in Peru's Cusco Valley during the 13th century, a royal Inca dynasty charmed, bribed, intimidated, or conquered its rivals to create the largest pre-Columbian empire in the New World.

For many years, scholars possessed few clues about the lives of Inca kings, apart from flattering histories that Inca nobles told soon after the arrival of Spanish conquistadores. The Inca had no system of hieroglyphic writing, as the Maya did, and any portraits that Inca artists may have made of their rulers were lost. The royal palaces of Cusco, the Inca capital, fell swiftly to the European conquerors, and a new Spanish colonial city rose on their ruins, burying or obliterating the Inca past. In more recent times, civil unrest broke out in the Peruvian Andes in the early 1980s, and few archaeologists ventured into the Inca heartland for more than a decade.

Now archaeologists are making up for lost time. Combing rugged mountain slopes near Cusco, they are discovering thousands of previously unknown sites, shedding new light on the origins of the Inca dynasty. Gleaning clues from colonial documents, they are relocating the lost estates of Inca rulers and examining the complex upstairs-and-downstairs lives of imperial households. And on the frontiers of the lost empire, they are piecing together dramatic evidence of the wars Inca kings fought and the psychological battles they waged to forge dozens of fractious ethnic groups into a united realm. Their extraordinary ability to triumph on the battlefield and to build a civilization, brick by brick, sent a clear message, says Dennis Ogburn, an archaeologist at the University of North Carolina at Charlotte: "I think they were saying, 'We are the most powerful people in the world, so don't even think of messing with us.'"

On a sun-washed July afternoon, Brian Bauer, an archaeologist from the University of Illinois at Chicago, stands in the plaza of the sprawling Inca ceremonial site of Maukallacta, south of Cusco. He takes a swig of water, then points to a towering outcrop of gray rock to the east. Carved into its craggy summit are massive steps, part of a major Inca shrine. Some 500 years ago, Bauer says, pilgrims journeyed here to worship at the steep outcrop, once regarded as one of the most sacred places in the empire: the birthplace of the Inca dynasty.

Bauer, a wiry 54-year-old in a battered ball cap and blue jeans, first came to Maukallacta in the early 1980s to uncover the origins of the Inca Empire. At the time most historians and archaeologists believed that a brilliant, young Andean Alexander of Macedonia named Pachacutec became the first Inca king in the early 1400s, transforming a small collection of villages into a mighty empire in just one generation. Bauer didn't buy it. He believed the Inca dynasty had far deeper roots, and Maukallacta seemed the logical place to look for them. To his bewilderment, two field seasons of digging turned up no trace of primeval Inca lords.

So Bauer shifted north, to the Cusco Valley. With colleague R. Alan Covey, now an archaeologist at the University of Texas at Austin, and a team of Peruvian assistants, he marched up and down the steep mountain slopes in straight transect lines for four field seasons, recording every scattering of pottery sherds or toppled stone wall he came across. Persistence paid off. Bauer and his colleagues eventually discovered thousands of previously unknown Inca sites, and the new evidence revealed for the first time how an Inca state had risen much earlier than previously believed—sometime between 1200 and 1300. The ancient rulers of the region, the mighty Wari (Huari) lords who reigned from a capital near modern Ayacucho, had fallen by 1100, in part due to a severe drought that afflicted the Andes for a century or more. In the ensuing turmoil, local chiefs across the Peruvian highlands battled over scarce water and led raiders into neighboring villages in search of food. Hordes of refugees fled to frigid, windswept hideouts above 3,962 meters (13,000 feet).

But in the fertile, well-watered valley around Cusco, Inca farmers stood their ground. Instead of splintering apart and warring among themselves, Inca villages united into a small state capable of mounting an organized defense. And between 1150 and 1300, the Inca around Cusco began to capitalize on a major warming trend in the Andes.

As temperatures climbed, Inca farmers moved up the slopes by 244 to 305 meters (800 to 1,000 feet), building tiers of agricultural terraces, irrigating their fields, and reaping record corn harvests. "These surpluses," says Alex Chepstow-Lusty, a paleoecologist at France's Centre for Bioarchaeology, University of Montpellier 2, who has been studying the region's ancient climate, allowed the Inca to "free up many people for other roles, whether building roads or maintaining a large army." In time Inca rulers could call up more conscripts and supply a larger army than any neighboring chief.

With this big stick, Inca kings began eyeing the lands and resources of others. They struck marriage alliances with neighboring lords, taking their daughters as wives, and dispensed generous gifts to new allies. When a rival lord spurned their advances or stirred up trouble, they flexed their military might. In all the surrounding valleys, local lords succumbed one by one, until there was only one mighty state and one capital, the sacred city of Cusco.

Flush with success, Inca kings set their sights farther afield, on the wealthy lands surrounding Lake Titicaca. Sometime after 1400, one of the greatest Inca rulers, Pachacutec Inca Yupanqui, began planning his conquest of the south. It was the dawn of empire.

Massed on a high, cold Peruvian plain north of the great lake in the mid-1400s, the army of the Colla people bristled with battle gear, daring the Inca invaders to make war. Pachacutec scanned the enemy ranks in silence, preparing for the great battle ahead. The lords of the Titicaca region ruled as many as 400,000 people in kingdoms arrayed around the lake. Their lands were rich and desirable. Gold and silver veined the mountains, and herds of alpacas and llamas fattened in lush meadows. Military success in the Andes depended on such livestock. A llama, the only draft animal on the continent, could carry 31.7 kilograms (70 pounds) of gear on its back. Llamas, along with alpacas, also provided meat, leather, and fiber for clothing. They were jeeps, K rations, and fatigues all rolled into one—crucial military assets. If the Inca king could not conquer the Titicaca lords who owned these vast herds, he would live in fear of the day these lords would come to conquer him.

Seated on a shimmering litter, Pachacutec issued the order to attack. Playing panpipes carved from the bones of enemies and war drums fashioned from the flayed skins of dead foes, the Inca soldiers advanced toward the Colla forces, a moving wall of terror and intimidation. Then both sides charged. When the fog of battle lifted, Colla bodies littered the landscape.

In the years that followed, Pachacutec and his descendants subdued all the southern lords. "The conquest of the Titicaca Basin was the jewel in the crown of the Inca Empire," says Charles Stanish, an archaeologist at the University of California, Los Angeles. But military victory was only the first step in the Inca's grand strategy of empire building. Officials next set about establishing civil control.

If provinces mounted resistance, Inca sovereigns reshuffled their populations, deporting restive inhabitants to the Inca heartland and replacing them with loyal subjects. Residents of remote walled villages were moved to new Inca-controlled towns sited along Inca roads—roads that sped the movement of Inca troops. Inca governors ordered the construction of roadside storehouses for those troops and commanded local communities to fill them with provisions. "The Inca were the organizational geniuses of the Americas," Stanish says.

Under Inca rule, Andean civilization flowered as never before. Inca engineers transformed fragmentary road networks into interconnected highways. Inca farmers mastered high-altitude agriculture, cultivating some 70 different native crops and often stockpiling three to seven years' worth of food in vast storage complexes. Imperial officials excelled at the art of inventory control, tracking storehouse contents across the realm with an ancient Andean form of computer code—colored and knotted cords known as quipus. And Inca masons raised timeless architectural masterpieces like Machu Picchu, which continues to awe visitors today.

By the time the Inca King Huayna Capac took power around 1493, little seemed beyond the reach of the Inca dynasty. To bring grandeur to his new capital in Ecuador, Huayna Capac put more than 4,500 rebellious subjects to work hauling immense stone blocks all the way from Cusco—a distance of nearly a 1,609 kilometers (1,000 miles) up and down dizzyingly-high mountain roads. And in the Inca heartland, a small army of men and women toiled to construct a royal estate for Huayna Capac and his family. At the king's bidding, they moved the Urubamba River to the southern side of the valley. They leveled hills and drained marshes, then planted corn and other crops, such as cotton, peanuts, and hot peppers, from far corners of the empire. In the center of the estate, they laid stones and bricks for Huayna Capac's new country palace, Quispiguanca.

As the late afternoon sun slants down, I wander the ruins of Quispiguanca with Alan Covey, the archaeologist from the University of Texas. Situated on the outskirts of the modern town of Urubamba, Quispiguanca basks in one of the warmest and sunniest microclimates in the region, which provided the Inca royal family a welcome escape from the cold of Cusco. The estate's gatehouses now look out on a field of pungent cilantro, and its surviving walls enclose a royal compound that once sprawled over an area equivalent to some seven soccer fields.

Encircled by parkland, fields, and gardens, Quispiguanca was an Inca version of Camp David, a retreat from the world, a place for a warrior-king to unwind after military campaigning. Here Huayna Capac entertained guests in the great halls and gambled with courtiers and other favorites, while his queen gardened and tended doves. The grounds boasted a secluded lodge and a forest reserved for hunting deer and other game. In the fields hundreds of workers cleared irrigation channels, raised and mended terrace walls, and sowed corn and a host of exotic crops. These provided Huayna Capac with bountiful harvests and enough corn beer to entertain his subjects royally during Cusco's annual festivals.

Quispiguanca was not the only spectacular estate. Inca kings inherited little more than their titles, so each new sovereign built a city palace and country home for himself and his lineage shortly after assuming power. To date archaeologists and historians have located ruins of roughly a dozen royal estates built by at least six Inca kings.

Even after these kings died, they remained the powers behind the throne. "The ancestors were a key element of Andean life," says Sonia Guillén, Peru's minister of culture. When Huayna Capac perished of a mysterious disease in Ecuador around 1527, retainers mummified his body and carried it back to Cusco. Members of the royal family frequently visited the deceased monarch, asking his advice on vital matters and heeding the replies given by an oracle sitting at his side. Years after his death, Huayna Capac remained the owner of Quispiguanca and the surrounding estate. Indeed, royal tradition dictated that its harvest keep his mummy, servants, wives, and descendants in style for eternity.

It was during the rainy season in 1533, an auspicious time for a coronation, and thousands of people were packed into the main plaza of Cusco to celebrate the arrival of their new, teenage king. Two years earlier, amid a civil war, foreign invaders had landed in the north. Metal-clad and bearing lethal new weapons, the Spaniards had journeyed to the northern Inca town of Cajamarca, where they imprisoned the Inca king, Atahuallpa. Eight months later, they executed their royal captive, and in 1533 their leader, Francisco Pizarro, picked a young prince, Manco Inca Yupanqui, to rule as a puppet king.

In the far distance, voices of the young king's bearers echoed through the streets, singing songs of praise. Falling silent, celebrants watched the royal teenager enter the square, accompanied by the mummies of his ancestors, each richly attired and seated on a splendid litter. The wizened kings and their consorts reminded all that Manco Inca descended from a long line of kings. Rulers of other realms might content themselves with displaying carved or painted images of their glorious ancestors. The Inca kings went one better, displaying the expertly preserved bodies of their forefathers.

In the months that followed, the Spanish invaders seized the palaces of Cusco and the spacious country estates and took royal women as mistresses and wives. Incensed, Manco Inca rebelled, and in 1536 tried to drive them from the realm. When his army suffered defeat, he fled Cusco for the jungle city of Vilcabamba, from which he launched guerrilla attacks. The Spanish wouldn't subdue the stronghold until 1572.

In the turmoil of those decades, the Inca's sprawling network of roads, storehouses, temples, and estates slowly fell into ruin. As the empire crumbled, the Inca and their descendants made a valiant attempt to preserve the symbols of imperial authority. Servants collected the precious bodies of the sacred kings and concealed them around Cusco, where they were worshipped in secret—and in defiance of Spanish priests. In 1559 Cusco's chief magistrate, Juan Polo de Ondegardo, resolved to stamp out this idolatry. He launched an official search for the bodies, questioning hundreds. With this information he tracked down and seized the remains of 11 Inca kings and several queens.

For a time colonial officials in Lima displayed the mummies of Pachacutec, Huayna Capac, and two other royals as curiosities in the Hospital of San Andrés in Lima, a facility that admitted only European patients. But the damp coastal climate wreaked havoc with the bodies. So Spanish officials secretly buried the greatest of the Inca kings in Lima, far from the Andes and the people who loved and worshipped them.

In 2001, Bauer and two Peruvian colleagues, historian Teodoro Hampe Martínez and archaeologist Antonio Coello Rodríguez, went looking for the mummies of the Inca kings, hoping to right a historic wrong and restore to Peruvians an important part of their cultural heritage. "Can you imagine," Bauer asks, "how American citizens would feel if the British had taken the bodies of the first several presidents back to London during the War of 1812?"

For months Bauer and his colleagues pored over old architectural plans of the Hospital of San Andrés, now a girls' school in central Lima. Eventually they identified several possibilities for the burial site of Pachacutec and Huayna Capac. Using ground-penetrating radar, they scanned the likeliest areas, turning up what appeared to be a vaulted underground crypt. Bauer and his Peruvian teammates were thrilled.

When the archaeologists finally dug down and opened the door of the dusty chamber, they were crestfallen. The crypt lay empty. Quite possibly, Bauer says, workmen removed the contents while renovating the hospital after a severe earthquake. Today no one can say where Peru's greatest kings lie. Bauer sadly concludes, "The fate of the royal Inca mummies remains unknown."