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They started finding the bodies right away.

In November of 2006, excavation began on 4.2 acres near North Stone Avenue and East Alameda Street, site of a planned joint city/county courts complex. • It would last 16 months. • It would also turn out to be one of the largest single historic excavations in the country.

"We were totally unsure when we started how many bodies we would find there," says Roger Anyon, program manager for Pima County's Cultural Resources and Historic Preservation Office. "We thought maybe a couple of hundred would be left."

Instead, they uncovered 1,082 graves, along with almost 1,400 bodies — 1,044 of them complete, the rest portions of bodies disturbed by development.

"There's been more than 100 years of destruction and building there," says Anyon. "People dug pits, put in water, sewer, gas and electric lines. Bones were dug up, mixed up and put back together.

"When TNI (Tucson Newspapers Inc.) took out their basement by bulldozer, some of that dirt was used as fill in city alleys. That's how we did things in the '40s and '50s. Things change."

Do they ever.

When this excavation began, a backhoe with a smooth-edged back allowed the operator to skim dirt at less than 1-inch levels.

"When we saw the stain of a grave pit, we'd then excavate by hand," says Anyon.

Archaeologists from Statistical Research Inc., which was hired for the job, uncovered crosses and coffin nails, but little clothing.

"We did find buttons and a number of pairs of shoes with the individual," says Anyon. "Sometimes we found people with lead shot in them. Tucson was a violent town."

They also found a high number of children.

"In one or two instances, we found mother and child together," says Anyon.

But before one bucket of earth could be sifted, the cemetery and its history were painstakingly researched, beginning in early 2005, also by Statistical Research.

"We did two background studies," says Anyon. "We tried to find all the potential descendant groups: Asian, Hispanic, Indian." Figuring most of the dead were Hispanic and Catholic, they pored through Diocese of Tucson death records, trying to get a sense and size of the population.

"For this particular cemetery, there are death records from the diocese and from the government, but no burial records," says Marlesa Gray, Statistical Research's director of historic programs. "They may have buried them with a plan, but there was no plan recorded."

Records indicated that most Indians in the area were transported to Mission San Xavier del Bac for burial.

The county also worked with the Arizona State Museum to determine who might be affiliated with the cemetery, says John Madsen, the museum's associate curator of archaeology and repatriation coordinator.

"We tried to identify as many groups that might have been interested and called them in for consultation," says Madsen, who met with Los Descendientes del Presidio de Tucson and several Indian groups. He also advertised for months, locally and nationally, trying to get the word out.

From those meetings came certain conditions: "No photos of the (graves) excavation, no destruction of anything, no DNA, because that destroys the bone," says Anyon.

Armed with a court order to excavate, along with a state permit to disinter and re-inter human remains, excavation finally began on Nov. 6, 2006.

The property also held four empty buildings, including a one-time bowling-alley-turned-bank used for a time by the excavation team as an office.

"As they needed to excavate, they would tear down a building and start the work," says Anyon. "A lot more than archaeology was involved."

Archaeologists also uncovered several privies from homes built on the site, as well as two pre-Hohokam pit houses.

"We expected that because in a sense you can find that anywhere," says Gray.

What was unexpected was the size of this graveyard. "We were all surprised at how extensive the cemetery was," says Gray.

Lynne Goldstein, professor of anthropology at Michigan State University and a consultant on the job, says, "Most large cemeteries excavated were pauper cemeteries. This cemetery is so interesting because it tells us so much more. It's truly a cross section of Tucson."

Graves ranged from a few inches below the surface to 8 feet deep, with most between 3 and 6 feet deep. "Some were very shallow. We took the tarmac off the parking lot and found human remains right under it," says Anyon.

"We carefully uncovered the entire individual, mapped everything, how the person was laid out, what position. We used a scanning device that gives a detailed image of the individual. After completing that, we removed all the bones and funerary objects."

Remains were taken to an on-site lab, to be examined by osteologists, experts in studying the function and structure of bones.

Even minus DNA testing, the bones, says Anyon, revealed everything from age and sex to what disease may have killed the person. "We found a whole host of information."

"There are certain bones that are more likely to give you information than others," says Gray. "You can't tell sex or age from a femur. Pelvic bones or the cranium provide the most data."

Archaeologists also found remains from the military portion of the cemetery, though most bodies were removed in 1884.

Those remaining — 70 in all, including some who were perhaps family members of soldiers — are to be reburied in 2009 at the Southern Arizona Veterans Memorial Cemetery in Sierra Vista, says Anyon.

Before that happens, work will go on to try to identify those individuals through military records and maps, says Anyon. Work on identifying civilian remains — for instance designating cultural affinity — also will continue, he adds.

In May of 2009, all civilian remains from the site, including those stored at the Arizona State Museum, are scheduled to be reburied at Tucson's All Faiths Cemetery.

So far, the cost of all this is around $15 million. "It sounds like a lot, but it's an average price for this kind of job," says Anyon. The job includes research, documentation, excavation, demolition of buildings, tearing up of streets and removal and replacement of sidewalks.

"We did find parts of bodies underneath the sidewalk on Stone Avenue, but none of the bodies extended into Stone Avenue or under Alameda," says Anyon, adding that bodies might still lie beneath a parking lot serving Chicanos por la Causa, 200 N. Stone Ave.

During the excavation, a transformer had to be removed and replaced in that parking lot.

"That automatically became a dig," says Tillie Arvizu, vice president of Chicanos por la Causa. Two graves were found, one intact, one exhumed.

Other than that, Anyon is reasonably sure all the bodies have at last been removed from the old National Cemetery.

Madsen is not so sure. "The cemetery was a lot larger than what is being removed now. I have to be cautious, but as soon as they stick a backhoe trench by the railroad tracks, they may find something."

The land was home to many things over the years — houses and businesses alike. But for a brief period of time, only the dead were here.

Beginning around 1862, a barren plot of ground stretching north and east from North Stone Avenue and East Alameda Street to East Toole Avenue served as the city's only official graveyard.

Known as the National Cemetery, it received during its time perhaps as many as 2,000 bodies. Besides civilians, the cemetery took in the remains of soldiers stationed Downtown at what was then Camp Lowell.

In 1875, two years after Camp Lowell moved to Fort Lowell, the cemetery was closed to civilian burials, although military burials were allowed until 1881.

In 1884, military remains were removed and reburied at Fort Lowell, before final burial in 1892 in San Francisco.

Meanwhile, survivors of all those civilians buried at National Cemetery were urged to remove their loved ones to the new Court Street Cemetery — bounded by Speedway, Main Street, Stone Avenue and Second Street.

Some did, many didn't.

As time passed, many of the graves were disturbed, prompting the Arizona Weekly Star on Feb. 3, 1881, to complain about open graves and coffins with bodies "in various stages of decomposition," as well as "skeletons exposed to view."

With the city absolving itself of responsibility, some of the families did hire a local undertaker to remove their loved ones, but it appears most of the bodies remained.

"Once you buried people, you presumed they would be left alone," says Fred McAninch, committee chairman of Los Descendientes del Presidio de Tucson.

Because many of Los Descendientes' ancestors were presumed buried at National Cemetery, the committee was consulted prior to excavation.

Los Descendientes member Armando Elias, 81, whose Tucson ancestors go back to 1797, has counted 20 of his relatives who died during the time National Cemetery was in use.

Arnold Smith, who counts Presidio commandant José Maria Martinez as his oldest Tucson relative, also estimates about 20 from his family may have been buried at National Cemetery. "I have no idea where they were."

McAninch theorizes that many Tucsonans were illiterate and did not see the removal notices published in the local papers in Spanish and English.

"Very few of the graves were empty," says McAninch. "The vast majority were still there."

Lynne Goldstein, professor of anthropology at Michigan State University and consultant on the project, says our attitudes about death were different then.

"We always cared about our loved ones, but we did not go to the graves on a regular basis. The people who were buried there were buried with care and deliberation. But we felt when people were buried, they were gone. We moved on."

In 1880, the railroad came to town, its tracks slicing across the northeast corner of the cemetery, though it appears no burials occurred there.

Nine years later the city began selling lots within the old cemetery and by 1900 it had become largely residential.

By 1930, however, the area was turning to commercial use. In 1940, Tucson Newspapers Inc. erected a large two-story building with a basement. Excavation for the basement uncovered at least one skeleton.

Additional excavation for an expansion of TNI in 1953 uncovered the skeletal remains of between 80 and 120 individuals.

Of those, 49 are stored at the Arizona State Museum, says museum osteologist John McClelland. As for the rest: "Quite possibly some were so badly disturbed they weren't brought to the museum," he adds.

The 49, along with those found during the more recent excavation, will be reburied at Tucson's All Faiths Cemetery.

Perhaps then, all will have found a final resting place.

A smallpox epidemic swept through Tucson in the spring of 1870, taking 78 lives by year's end, many of them infants.

It was by far the biggest killer that year, according to the 1870 Federal Census Mortality Schedule, which lists the deaths of 139 Tucsonans.

Many are presumed to have been buried at National Cemetery.

Second to smallpox as cause of death was "Killed by Indians," as succinctly noted in the report. Among the 14 dead: freighter E.G. Pennington, 60, and his son, E.G. Jr., 20, who were buried out of town. Downtown's Pennington Street is named for the family.

Pneumonia came in next, with 13 deaths, followed by malarial fever, at nine deaths.

Four died from "pistol shot," including gambler William Sloan, who aimed for his own head and did not miss.

Eighty of the dead were children under the age of 10, with 30 of them infants ages 1 and under. Only four who died made it past 45, including Taresio Basques, 80, a brick mason from Guadalajara.

The dead were born in Kentucky and Ohio, New York and Texas, Illinois and California. One was born in Ireland, a Mary O'Neil, whose occupation is listed as "keeping house." Dead at 30. Same for Albert Dick, a watch repairer from Switzerland.

Most of the dead, 60, were born in what was by 1870 called Arizona. Forty-one were born in Sonora. Two were listed as black, two as Indians, the rest white. Of those, 100 had Hispanic surnames.

In life they were farmers and laborers, carpenters and clerks, freighters and miners, wagonmasters and gamblers, cooks and seamstresses.

All had one thing in common: They all died in the same year, in the small frontier town of Tucson, Arizona.