On a cool spring day, in the bewitching crystalline light for which New Mexico is famous, I stood in the middle of the Acoma Sky City and looked out into the ocean of desert at an island of pale red and dun colored rock called Enchanted Mesa.

My tour guide, Marissa Chino, a young Acoma woman, said it isn’t known if her people once lived there. There are tales, though, that say they did. One story holds they descended to the valley to tend their squash and corn and, while they were farming, a violent storm washed away a stone ladder that was their only access. With no way back up the monolith, they abandoned their home and moved to the 357-foot tall mesa where the village sits now.

This is only one of the great many mysteries about the ancient Puebloan civilization that once flourished across the desert landscape of the American Southwest and, for a long time, was believed to have vanished.

Its fate has become clearer in recent years, as researchers have peered more deeply into where this civilization went on its “final migration” and listened more closely to the descendants of those once called the Anasazi — Navajo for Enemy Ancestors — who are now known as ancestral Puebloans.

I traveled to the red rock desert of the Southwest to better understand this “lost” civilization. It took some winnowing, as there are numerous parks and monuments to visit. I chose to focus on several major sites in northern New Mexico and southwestern Colorado.

To start, from Albuquerque I drove an hour to Sky City and stopped at the impressive visitor center, which includes the Haak’u museum with its collection of Acoma pottery. Two buses carried me and a group of 30 or so leather-jacketed Norwegian motorcyclists on a short ride to the collection of houses at the top of the giant mesa. This low-slung, earth-colored village, with its rough and uneven stone streets, is one of the four communities that make up the Acoma Pueblo, which is one of the state’s 19 modern-day pueblos. Sitting in an immense and surreal landscape, with its broad palette of dusky reds and browns beneath a vast sky, it is one of the most sublime settings for a town in North America.

Acoma means “people of the white rock,” and Sky City is one of the longest inhabited settlements in North America, tracing its founding to around 1100 A.D. Between 10 and 13 families live here in small and neatly kept adobe homes. Water must be hauled in, and there is no electricity.

For an hour I followed our guide around the ancient village. Beehive-shaped clay pottery kilns, fired with wood or cow dung, sit behind the homes, with piles of firewood stacked alongside. The inimitable southwest fragrance of sweet burning pinyon pine wafted in the air.

We walked toward the towering adobe, dirt-floor church. A graveyard surrounded by a crude adobe wall sits in the front of the church where Acoma people are buried several layers deep. The top is studded with a mix of white wooden crosses, stone tablets and plastic flowers.

Spanish conquistadores came to this region in the 16th century seeking the fabled Seven Cities of Gold. Francisco Vásquez de Coronado showed up first, in 1540, but others followed, and as we stood inside the church our guide related some of the grim history of Acoma. After a small battle with soldiers sent to negotiate, the conquistador Don Juan Oñate attacked the mesa and killed hundreds of men, women and children. He took 500 prisoners and sentenced those over 25 to 20 years of servitude. He ordered the right feet and hands of some two dozen captives amputated.

The Acoma people returned here after their servitude, and in 1628, the Catholic Church forced them to build this structure, the San Esteban del Rey Mission church — an unusual blend of Spanish colonial and Puebloan architecture. All of the materials, including the logs and dirt for the walls, had to be found elsewhere and carried up from the valley floor. It took 12 years to build.

Just as I began to walk back to the visitor center, down the narrow and precipitous stone path that the Acoma used before the road was built in 1929 by a film company, our guide pointed out a small, opaque mica window in one of the homes. The window glints in the sun like gold, she said, and when the Spanish saw it they thought they’d found one of the legendary Seven Cities of Gold. It is the only original mica window that remains here.

The Pueblo culture goes back centuries before the time of Christ. Pueblos evolved from pit houses — holes in the ground covered with a raised wooden roof — to labyrinthine dwellings with hundreds of rooms built with strikingly sophisticated masonry techniques, that peaked in the 10th and 11th centuries.

What’s been recognized in recent years is that the Ancestral Puebloans didn’t vanish. Whether because of a withering drought, deforestation and soil erosion, or attacks from other tribes, or a combination of these things, their vast empire shrank and became the pueblos of New Mexico.

The great houses of Chaco Canyon

I drove north from Acoma, seeking out more back story. Two hours on — the last half of it on a rutted, severely wash-boarded dirt road — I spied Fajada Butte, the towering landform at the head of a long, shallow sandstone canyon called Chaco, now the Chaco Culture National Historical Park.

First occupied in 800, Chaco was where the Pueblo culture reached its greatest heights until, tree rings tell us, it was abandoned in the mid-13th century. The park contains the largest collection of pre-Columbian ruins in the United States and is a UNESCO World Heritage site.

While most American Indians were hunters and gatherers, the Puebloans were also accomplished tillers of the soil, irrigating the wild desert in this canyon with captured rainwater. Staying in one place for long periods is a large part of what allowed this civilization to evolve to such a magnificent apogee in a harsh desert landscape.

I toured Pueblo Bonito with Clif Taylor, a knowledgeable Park Service volunteer who has spent 12 seasons here. Taylor is a fount of information, yet is only able to scratch the surface on a two-hour tour. He too is taken with the mystery of this place. For centuries it was home to thousands of people and “over a few decades it virtually emptied out,” he said.

Pueblo Bonito is the largest and grandest of the 12 “great houses” at Chaco, with some 600 rooms and 40 kivas, which are large, round ceremonial rooms dug into the earth and lined with stone masonry.

The evolution of the ancestral Puebloans is mirrored in the evolution of their masonry, from pit-houses where the foundation was made of rocks roughly stacked atop each other, to the structures at Chaco, where many millions of pieces of stone, ranging in size from a deck of cards to a large book and larger, are fitted precisely together up to five stories high. More than 240,000 trees, cut in the distant mountains, were used in construction of the great houses of Chaco.

The remains of the massive D-shaped structure of Pueblo Bonito, which covered 2½ acres, has been a treasure trove for archaeologists since the late 19th century.

The artifacts uncovered here boggle the mind. A few from the long list: hundreds of gorgeous ollas or large round pots, clay ladles, bowls, animal effigy pots and other vessels covered with black geometric designs over a white slip. There are the sumptuous burials of 37 sacred macaws, the gorgeous red, blue, yellow and green parrots, brought here from southern climes and likely bred for their rainbow of resplendent sacred feathers.

A jet frog, black as coal and the size of a child’s fist, with inlaid turquoise eyes and a turquoise collar, is one of the most prized artifacts from Chaco, likely a rain fetish.

Then there is the mystery of Room 33.

That’s where two high status individuals — “major dudes’,” according to one archaeologist — were found buried beneath a wooden platform with another dozen remains scattered in the sand above them. No one knows who they were. The room also contained more than 50,000 pieces of turquoise, 6,000 pieces of worked shell, turquoise-encrusted conch shell trumpets and a collection of carved wooden flutes.

The ability to appreciate the beauty and mystery of a giant buzzing pre-Columbian capital in Chaco is enhanced by the isolation and minimal development. It is quietly exhilarating to wander in the sunshine among the glorious remnants of such an elaborate and alien city, with just a scattered handful of other visitors. You can almost hear the barking dogs, the calls of a bevy of children and the gobbling of turkeys that once wandered here.

As I walked I noticed a distant storm and a trail in the sky of lace-like virga, or shafts of rain that hang from a cloud, never making it to the ground.

At night here, with the lights of cities far away, the sky is a midnight fabric stitched with glowing glass beads.

Archaeoastronomers — those who study how ancient people related to the sky — tell us that many of the walls and windows at Chaco are aligned with cardinal points, the sun and other stars, and the buildings functioned as an observatory and calendar. Then there’s the famous sun dagger. On the summer solstice a sharp beam of light shines through slabs of fallen rock and pierces the exact center of a spiral petroglyph.

Despite what is known here, what exactly this fantastic city was remains unknown, and the mystery endures. “It was built to be impressive,” Taylor said. “A big beautiful city like Manhattan. It may well have been an area of transcendental significance like Mecca. The canyon itself could have been a sipapu,” a sacred opening in the earth that are symbolically represented in kivas around the Southwest.

The characters who were entranced by the mystery of these ruins and the vanished people, and who excavated and explored these places, have their own interesting stories. Richard Wetherill is the most well known, the son of a rancher, who, when he first spied treasures in the ground, leapt off his horse and began digging. He never stopped.

An accomplished amateur archaeologist, Wetherill led an expedition here in 1896, funded by two wealthy young brothers, Talbot and Frederic Hyde. The first year Wetherill unearthed a boxcar full of artifacts, Taylor told me. “They shipped them back East and they are housed in the basement of the American Museum of Natural History.”

There has been much plundering of the sites here and across the Four Corners region by profiteers. The Antiquities Act of 1906, which protects property on federal lands (and allows the president to unilaterally create national monuments without consulting Congress) was initiated because of the theft of artifacts from Chaco.

The cliff dwellings of Mesa Verde

After a day of hiking around Chaco I tooled north a few hours, heading for the ruins of another great Puebloan civilization, at Mesa Verde National Park.

Chaco’s structures were built in the open canyon bottoms, but the people of Mesa Verde were largely cliff dwellers, likely as a way to fend off Apache, Ute and other raiders. Toe and hand holds that allowed access to the precipitous dwellings remain carved in the sandstone cliffs. The people farmed on the top of the mesa and lived in the dwellings.

From the visitor center I drove 15 miles to the top of Chapin Mesa to tour a series of sites that track the evolution of ancient home building. As I drove the vistas became more incredible, a vastness that stole my breath. I live in the big sky country of Montana, and I am no stranger to expansive views, but this was impressive.

A series of stops on the 6-mile loop provides a look at how the houses evolved over nearly seven centuries, from the seventh century to the 13th century, from pit houses to the sophisticated adobe and stone block buildings wedged into cliff alcoves, such as Oak Tree House, that reminded me for all the world of mud swallow nests.

My last stop was the Zia Pueblo, a half-hour from Albuquerque, to see what Peter Pino, a former war chief and cultural leader, had to say about the ancestral Puebloans he calls his grandfathers.

Pino graciously invited me into his home, and we sat on the couch to talk. I spied some Zia pottery, which famously features a bird motif. Why did so much of the pottery use it, I asked. “Birds occupy a region that we humans don’t — the heavens,” he said. “The world they see is a lot bigger than ours. To native people that is supernatural.”

The pueblos at Chaco and elsewhere are not cold and sterile piles of rock, he said, but alive with the spirit of the pueblo people’s ancestors. “All those sites are sacred,” Pino said. “They are places of significance to the pueblo people. Our people aren’t there anymore, but the spirits of our people are still there.”

Jim Robbins a frequent contributor to The New York Times. His most recent book is “The Wonder of Birds: What They Tell Us About Ourselves, The World and a Better Future.”