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On a recent, unusually warm late-winter day, a young woman sat quietly at the foot of a white headstone at Arlington National Cemetery, among a cluster of graves of troops killed in Iraq and Afghanistan. The woman, maybe 25 years old, sat in the grass, hugging the headstone.

The question is not why she was doing that (that's easy to understand); the question is whether the headstone she was hugging was the right one. Last summer, an Army inspector general's investigation confirmed that the Army had effectively lost control of its sacred ground, the national resting place of John F. Kennedy, Audie Murphy and 330,000 others who faithfully served their country. The Army probe played down reports of misplaced or lost remains, but the revelations prompted congressional hearings and howls of disgust from veterans' organizations. In an unusual departure from the Army's normal reflexes, Army Secretary John McHugh pushed out the superintendent of Arlington and his deputy and installed a new boss to make things right on its hallowed site.

But it appears likely that the problems at Arlington are far worse than the Army has acknowledged, and the new chief, Kathryn Condon, admits the service may never be able to identify all the missing remains on the immaculate 624-acre (250 hectare) site. The Army now plans to make only educated guesses about the identity of remains rather than digging in the dirt to be sure. That means that the true location of some remains may be a mystery forever.

Mistaken Identities
The Army has known for months that it may have a massive case of mistaken identity on its hands — but has been reluctant either to admit it or to learn exactly how widespread the burial errors are. Through the Freedom of Information Act, TIME obtained the raw transcripts of interviews that cemetery workers gave in 2009 and 2010 to the inspector general. In contrast to the tepid report the IG released last June, the transcripts show how workers repeatedly found unidentified remains while digging in what were supposed to be empty graves. "We went into a grave site, which we assumed was empty," one worker recalls. "Dig down ...and, uh ... whoops! Another coffin." Another worker guessed that "one time out of 10," a headstone at Arlington sits above the wrong grave.

The idea of workers' unexpectedly coming across remains where none were supposed to be is troubling, but at least those remains can be identified. Many caskets buried at Arlington carry exterior identification tags. And for those that do not, rapid advances in DNA identification technology provide hope that almost any mystery can be solved.

The transcripts, however, show that an unknown number of cremated remains were placed in urns that are lost forever. The problem stems from Arlington's policy of burying spouses on top of each other. When a veteran or his loved one died and the remains were cremated, the urns were interred just 3 ft. (1 m) below ground. When Arlington workers returned later to prepare the grave site for a coffin burial of a spouse, they generally removed 7 ft. (2 m) of fill. Workers complained in the transcripts that they were sometimes not alerted that an urn was already in a grave before they dug there a second time. Urns were sometimes scooped up by backhoes and dumped into a landfill, where workers would occasionally come across them later by chance. "That happens a lot," one worker said. "Nobody knows until somebody happens to see it in the landfill and says, 'Oh, my God, man. We just screwed up.'"

And then there is Arlington's Civil War–era style of record keeping. Years after other massive cemeteries computerized all their burial records, Arlington still tries to track about 30 burials a day with bits of paper recording the names and locations of remains. (This antiquated system has persisted years longer than it should have because the previous Arlington leaders paid millions aimed at computerizing Arlington to a group of friendly contractors who did almost nothing in return.)

Graves at Arlington are generally numbered sequentially and grouped into sections that often consist of several thousand burial sites each. TIME has reviewed records and inspected headstones for more than a dozen of these sections, from brand-new burials to graves that date from the late 1800s. It is clear that burial errors are spread throughout the hundreds of thousands of graves at Arlington. In section 64, for example, the headstone for Army Specialist Chin Sun Pak Wells, who died at the Pentagon on Sept. 11, 2001, sits above grave No. 4642. But according to internal cemetery documents obtained by TIME, her grave card — one of two pieces of paper that show where her headstone should be — says she is in grave 4672. Similarly, the records for section 64 put the remains of Navy Commander Russell K. Wood Jr., Army Sergeant First Class Ernest F. Freeman and Air Force Lieut. Colonel Arthur Rolph in two separate graves each.

Mistaken identity at the cemetery takes still other forms. Arlington's paperwork, for example, says that in 2005, in that same section, Army Sergeant First Class Irving Havenner Jr. and Air Force Colonel George Drury were both buried in the same grave, No. 2605.

Kathryn Condon, the new Arlington boss and a career Army executive, won't acknowledge the scope of the problem but doesn't really deny it either: "I can't tell you if the problem is massive yet until we see where we have our discrepancies." Since taking over nearly a year ago, she says, she has implemented strict, six-step chain-of-custody standards for keeping track of remains buried today. Thanks to those steps, she says, the headstones erected since her arrival stand over the right graves.

As for past errors, Condon described an ambitious, years-long project to probe for potential mistakes. Hundreds of thousands of burial records will be digitized and compared with overhead images of the headstones in each section. Workers will then load into that database photographs of the front and back of each numbered headstone. Potential problems should pop up once all that data is compared. "That will tell us where we might have potential discrepancies," Condon explains, "or not."

But Condon also revealed a critical incongruity in her plans to "fix Arlington." She admits that the burial paperwork is an unreliable mess, yet at the same time she insists there is enough correct information in the documents to figure out the likely location of remains with some degree of accuracy — and without digging to make sure. Condon calls this the "presumption of regularity" in the paperwork. What she means is that when documents show one person buried in two places, for example, the cemetery could use ground-penetrating radar to figure out whether a particular grave contains remains or not. "When the headstone matches the records and we probe [with radar] and it all matches, you have to have a presumption of regularity that that is a correct grave site," she says.

The problem with this is that radar will tell the Army only if there is a casket in the ground, not who is in it. Condon admits that such judgments about who is buried where may turn out to be wrong. "The only way you are ever truly going to find out is to physically excavate," she acknowledges. Where cemetery records suggest that there are remains in two places, the Army could decide that the grave with the headstone that matches the name on the paperwork is probably the correct one. "We can validate through the records process," Condon explains.

Condon's strategy is to rely on the records and noninvasive tools to figure out the most likely identity and location of remains. She says she has already used this method to identify the remains in three mystery graves during her 10-month tenure. She cannot dig to confirm those judgments, she says, unless next of kin absolutely insist.

Leaving Some Behind
Condon knows from experience that digging sometimes leads only to new confusion. Last August, a skeptical widow steadfastly insisted that Arlington disinter the remains of her husband, an Army staff sergeant, from a grave in section 66 — even though the Army's records showed that her husband's remains were safely in that grave. His headstone also sat atop that site.

Arlington workers dug and found the remains not of the Army sergeant but of Jean Koch, wife of retired Air Force Colonel Bill Koch. And when Arlington workers dug under Jean Koch's headstone, which stood one grave to the left of the Army staff sergeant's headstone, they found no remains at all. So from Koch's headstone, they moved two graves over to the right. The headstone sitting there was marked as being for the wife of an unrelated Navy commander. They dug and found that Navy commander's wife's remains — along with the remains of the Army staff sergeant that officials were looking for in the first place.

It was a horrifying, domino-like series of burial mistakes, and it supports what people familiar with the cemetery's operations have long said: each burial error at Arlington might represent several related burial mistakes. Paul Bucha, who earned a Medal of Honor in Vietnam and who spends considerable time on veterans' issues, railed at the notion that Arlington would not determine beyond any shadow of doubt the correct identity and location of remains at the cemetery. "The question is, Which family will you look in the eye and swear that you know their loved one is buried there?" he asks.

Settling for an educated guess on the identity of remains, veterans say, flies in the face of the military's sacred leave-no-one-behind battlefield ethos. From the lowly Army private to the top Pentagon brass, the military has long stopped at nothing to bring a service member's remains home for honorable burial. Some 350 Pentagon employees work tirelessly in a program to track down combat remains wherever they may lie around the world. To help identify those remains, the Pentagon runs the largest high-tech forensic laboratory in the world, in Hawaii. "If you don't know who is in the ground," Bucha says, "how do you say no one is left behind?"

Bill Koch had previously visited the headstone of his wife Jean in section 66 only to learn last summer that her grave was empty. Contacted by TIME in Raleigh, N.C., Koch noted the irony of the military's pulling out the stops to identify a finger bone from the jungles of Vietnam but being reluctant to use a backhoe at Arlington. "They are never," he said, "going to fix the problem."

Award-winning journalist Mark Benjamin first broke the Arlington scandal in 2009 writing for Salon.com.

For a response to this story from the U.S. Army, click here

For Mark Benjamin's response to the Army, click here

• Mark Benjamin
• New evidence reveals serious burial mix-ups at Arlington National Cemetery. Does the Army want to fix the problem?