In a softly lit crypt beneath the chapel of the U.S. Naval Academy, a massive sarcophagus of veined marble rests on the backs of four bronze dolphins. At a respectful distance from the tomb, two midshipmen with gleaming swords stand vigil over a body and a mystery nearly as old as our country itself.

One hundred years ago, on April 24, 1906, amid pomp and fanfare the likes of which Annapolis had never seen, an American president laid to rest a national hero who had died more than a century before. The great man’s remains had only recently been returned to these shores, rescued from an unmarked grave in a foreign land—a discovery that was hailed, on two continents, as a triumph. Yet even at the time, there were whispers that the cadaver brought home in glory might be the wrong one. The whispers have never been completely silenced.

The stillness of the crypt is broken by the voice of a tour guide in Colonial costume. "John Paul Jones was truly a hero," she says. "He never lost a battle—came close, but he never lost." She tells the story of how he received the first salute offered by a foreign power to an American naval vessel, and how, in 1779, at the helm of the Bonhomme Richard, he captured the British frigate HMS Serapis even as his own ship sank beneath him—uttering the defiant cry, "I have not yet begun to fight!" She mentions his legendary good looks, his popularity with the ladies. "Jones died a relatively young man, at the age of 45," she says as she leads her group toward the exit.

She doesn't mention that a significant chapter of Jones' story began only with his death, and that it was more eventful than many people's lives.

In the spring of 1905, in a cramped, fetid tunnel beneath a working-class neighborhood of Paris, a group of men gathered around a battered coffin. Several of them were well dressed, in dark frock coats and bowler hats; others, in grimy, patched clothing, held picks and shovels. By the light of candles flickering around the head of the coffin, the men watched as its heavy lid was carefully removed. A sharp alcoholic odor arose, and the candlelight illuminated cloth and straw. Clearing away the wrapping, the men stared into the face of the corpse. "Paul Jones!" someone exclaimed, and all present solemnly removed their hats.

It was an especially satisfying moment for one of those frock-coated gentlemen: Gen. Horace Porter, the United States ambassador to France, for whom the discovery was the culmination of a tireless six-year quest.

Porter, too, was an American war hero. He had won the Medal of Honor at Chickamauga in 1863 and become one of Gen. Ulysses S. Grant’s favorite aides-de-camp, even standing at the Union commander’s side when Lee surrendered at Appomattox. When—after arriving in Paris in 1897—Porter learned that Jones' body had lain for more than a century in a forgotten grave somewhere beneath the city, he embarked on finding it in 1899 with the stamina of a veteran campaigner.

Over the years, other Americans had come to Paris in search of Jones, but had been thwarted by a lack of documents. The French records of his death and burial in 1792 had been destroyed in a fire; one searcher, in the 1850s, regretfully concluded that the hero’s bones had probably ended up in the vast Paris catacombs, lost forever among millions of anonymous skeletons. But through persistence and luck, Porter found an article with a transcript of the burial record. The article attested that Jones had been interred in the Cimetière St.-Louis, a small graveyard reserved for foreign-born Protestants.

But the cemetery itself seemed to have vanished. Finally, researchers hired by Porter unearthed old maps that located it along the rue Grange aux Belles in northeastern Paris. When Porter first visited the spot, he was appalled. The graveyard had apparently been closed shortly after Jones' burial, filled in, and built upon. The naval hero now lay somewhere beneath a laundry, a bric-a-brac shop, several ramshackle houses and a shed for the wagons of grain merchants. Amid these structures was a small, rubbish-strewn courtyard.

"Here," the ambassador later recalled, "was presented the spectacle of a hero whose fame once covered two continents...relegated to oblivion in a squalid quarter of a distant city, buried in ground once consecrated, but since desecrated by having been used at times as a garden, with the moldering bodies of the dead fertilizing its market vegetables, by having been covered later by a common dump pile, where dogs and horses had been buried, and the soil was still soaked with polluted water from undrained laundries, and, as a culmination of degradation, by having been occupied by a contractor for removing night soil."

Porter was determined to dig for the body at once, but one of his researchers conspired with local property owners to milk the rich American for all he was worth. "Fabulous prices" were demanded for the excavation rights, Porter wrote, and he ultimately had to "drop the matter entirely for a couple of years, to let the excitement subside."

Meanwhile, new impetus for the search was coming from the other side of the Atlantic, where Theodore Roosevelt had become president upon the assassination of William McKinley in 1901. T.R. was not just a lifelong naval history buff—he’d written his first book on the War of 1812 at sea—but had served as assistant secretary of the Navy and was an enthusiastic booster of the modern U.S. Navy, then basking in victories in the Spanish-American War. He immediately saw the propaganda value in a Jones resurrection, and let Porter know that if he wished to resume his quest, the federal government would pick up the bill.

Digging at the rue Grange aux Belles finally began in February 1905. Since the buildings there were not to be demolished, laborers had to dig shafts by hand, shoring them up with timbers as they went and hauling dirt to the surface with buckets and ropes. Almost immediately, they found what was left of the cemetery: reeking, viscous black soil studded with thousands of human bones—and sickeningly alive with enormous red worms. The men worked quickly. Photographs kept by Porter show piles of earth and cobblestones rising next to the laundry and the bric-a-brac shop and, down in the tunnels, skulls jumbled underfoot among heaps of bricks.

The workmen were looking for a leaden coffin: an old letter from an American acquaintance of Jones' who had been in Paris when the captain died said Jones had been buried in one, to preserve his remains in case America ever wished to reclaim them. After two and a half weeks of digging, they unearthed such a coffin, and newspapers reported that Jones had been found—until, the next day, a corroded nameplate on the casket revealed that it contained someone else. Over the next several weeks, other lead coffins would turn up, each bearing an unJonesian name or containing a skeleton of the wrong dimensions.

But, on the last day of March, a lead casket with no nameplate—and of superior workmanship—was found. It was opened in Porter's presence a week later to reveal a body in exceptional condition, apparently because the coffin had been filled with alcohol as a preservative before burial. The corpse was that of a middle-aged man, dressed in a simple linen cap, ruffled shirt and shroud, with his waist-length dark hair gathered up at the neck. In photographs at the Naval Historical Center in Washington, D.C., even the stubble on his chin is visible. One eye appears half open, as if in an eternal wink.

Under cover of darkness, the cadaver was transported to Paris’s École de Médicine, where the city’s most eminent anthropologists could examine it. They took measurements, performed dissections and, as Porter, his aides and family hovered anxiously, compared the body with known portraits and descriptions of Jones. (Sixty years later, the ambassador's great-nephew recalled, with a shudder, being urged to hold the corpse’s "soft and pliable" hand.) At last, the scientists proclaimed their unanimous judgment: it was indeed the object of their quest. The linen cap even bore a monogram that looked like a "J" when held upright, and a "P" when upside down.

Ambassador Porter telegraphed Washington: "My six years' search for remains of Paul Jones has resulted in success."

But how could the body of America's greatest naval hero—a man who enjoyed worldwide fame in his own lifetime—have vanished for more than a century?

That chapter of the story begins in a very different quarter of Paris, along a fashionable Left Bank street called the rue de Tournon. The place today looks much as it must have in the summer of 1792: a row of sandstone facades, neat and formal as an 18th-century engraving, sloping gently toward the Luxembourg Palace. In a third-floor apartment toward the middle of the block, above what is now a rare-book shop, is the room where John Paul Jones died.

His career had taken several turns in the decade since America had won its independence from Britain. When the Revolutionary War ended and the Continental Navy disbanded, Jones found himself turned ashore without a command—an intolerable situation for a born sailor who loved, above all political allegiances, the mingled aromas of salt air and cannon smoke. Moreover, the Scottish-born captain had spent only a few years of his life in America ("the country of my fond election," as he called it) and always felt more at home in Europe. So Jones—rather to the embarrassment of some admirers—turned from serving the New World's fledgling republic to serving the Old World's most hardened despotism: he enlisted as rear admiral under Catherine the Great of Russia in her war against the Ottoman Turks. Within a year and a half, though, he left Russia precipitously, after having been implicated in a sexual scandal involving a 12-year-old girl (not the first time his libido had gotten him into trouble ashore). By 1790, Jones was in Paris, hoping that the Colonies' old ally Louis XVI—or perhaps the newly inaugurated President Washington, to whom he also sent an entreating letter—would favor him with a military command.

But the French king, in that year after the fall of the Bastille, had more pressing business to attend to, as did Washington, apparently. So Jones, his health and spirit failing, was left waiting in the rue de Tournon. Gouverneur Morris, the snobbish American minister to France, had little patience with the importunate sailor—a mere gardener's son, by the way—who visited him far too often. "He has nothing to say," Morris wrote snidely in his diary, "but is so kind as to bestow on me all the Hours which hang heavy on his Hands."

Morris' journal entry for July 18, 1792, notes: "A Message from Paul Jones that he is dying. I go thither and make his will." After this tiresome business was complete, the American diplomat hastened off to dinner, and then to call upon his mistress. Finally, later that night, the couple brought a doctor to the rue de Tournon, where they found Jones facedown on the bed, already turning cold.

Although the unmarried and childless Jones was far from impoverished at the time of his death, Morris decided that he should be buried "in a private and economical manner." A French admirer ended up footing the bill for a respectable funeral, but it was hardly a send-off worthy of a world-renowned hero. The cortege wound its way through Paris, passing beneath the Porte St.-Martin and up a steep country lane toward the little Protestant cemetery. Despite the upheavals of the French Revolution—Louis was himself just six months away from the guillotine—an official state delegation paid its respects at the brief service. A few Americans who happened to be in Paris also turned up. Morris was too busy with preparations for a dinner party he was hosting that night.

Several weeks later—several weeks too late—a letter addressed to "John Paul Jones a citizen of the United States" arrived in Paris. President Washington had appointed him to a diplomatic post in the service of his adopted homeland.

How different was Jones' next public procession through Paris, in the summer of 1905, along the Avenue de l'Alma and the Champs Élysées. Resplendent battalions of French cavalry and infantry accompanied the coffin, along with high government officials and diplomatic staff. Hundreds of American sailors and marines in dress uniforms, including an honor guard handpicked for their height and good looks, also marched proudly. (Spectators thronged the streets, and Porter noted with satisfaction how the French ladies, when these bluejackets passed, exclaimed, "Quels beaux garçons!")

President Roosevelt, in his delight at Porter's success, had dispatched an entire squadron of American warships across the Atlantic to receive the body. "I have never seen so many flags—big ones, little ones, French, American—all fluttering in the breeze," an eyewitness recalled in the 1970s.

Jones' Annapolis memorial service was more splendid still. On April 24, 1906, much of Congress, the cabinet and the diplomatic corps gathered at the Naval Academy armory, along with French and American naval squadrons, the entire corps of midshipmen and thousands of onlookers. Looming above a casket at a flag-draped stage, Roosevelt hailed Jones' "indomitable determination and dauntless scorn of death" and seized the opportunity to address current politics. "Those of you who are in public life have a moral right to be here at this celebration today only if you are prepared to do your part in building up the Navy of the present," T.R. declared in trademark style, flashing his teeth and thumping the podium.

Porter, too, eulogized the hero he had brought home. "His honored remains will be laid to rest in this historic spot in a mausoleum befitting his fame, but his true sepulcher will be the hearts of his countrymen," he told the assembled throng.

Yet amid all the hoopla, murmurs of skepticism were already audible. "There are many doubting Thomases who are not satisfied with the identification" of Jones' remains, The Literary Digest editorialized in its July 29, 1905, issue.

At least one such Thomas could be found in T.R.'s own cabinet. After Jones' return to America but before the commemoration, Secretary of the Navy Charles Bonaparte sent one of his aides to ask acting Secretary of State Alvey Adee for an independent autopsy before reburial. Hearing this request, the aide later recalled, Adee leapt up and ran into Bonaparte's office, from which "a strange bellowing sound" shortly emerged. As soon as the acting secretary of state had departed, the aide continued, Bonaparte "called me in to his office, and said that he had decided not to have any examination of Jones' body made at this time."

Several years later, art historians Charles Henry Hart and Edward Biddle published the most thorough attack yet on Porter's methods. They revealed that one of the two life busts of Jones by Jean Antoine Houdon that the French scientists had used for comparison with the corpse was not a portrait of Jones at all. As for the other, indisputably genuine bust, Porter's team had made much of the fact that its dimensions almost precisely fit the corpse's—perhaps too much, since Houdon was an artist, not an anatomist, and would not necessarily have strived for an exact match. Moreover, Hart and Biddle questioned the accuracy of the biography of Jones from which Porter had drawn his physical descriptions.

When journalists showed up at Porter's doorstep asking for a response—he had returned by then to New York City—he at first refused to comment, then gave a terse rebuttal to Hart and Biddle's points. Meanwhile, another writer suggested sarcastically that the tomb of the “unknown French gentleman” in Annapolis should bear the following inscription, in parody of Shakespeare’s famous epitaph:

Good friend, for Porter's sake, forbear
To doubt the dust inclosed here.
Blest be the man that got these bones,
And curst be he that says "'tain't Jones."

One afternoon not long ago, I made my way through the streets of Paris toward rue Grange aux Belles. I knew that the rue de Tournon house where Jones had died was still intact, but I had no idea what I would find at the spot where he spent the next hundred years.

The first signs were encouraging. The little street still rises in a lazy uphill curve, reminiscent of the country road it had been in 1792. And as in 1905, the quarter remains unfashionable, with office-supply shops, cheap jazz bars and florists specializing in plastic funeral wreaths. My hopes lifted even higher as I recognized the somber gray bulk of the 17th-century Hôpital St.-Louis on my right.

Then I rounded the curve and saw the site of numbers 43, 45 and 47. The corner bar across the street was still intact, exactly as I’d glimpsed it in some of Porter’s photographs—but the laundry, curiosity shop and wagon shed were gone, obliterated by a 12-story apartment building with an underground garage.

So if Horace Porter did get the wrong man, there is not much hope now that the right one could ever be found. The question is: How much faith should we have in his research, and in the forensic science of a century ago?

In 2004, Nikki Rogers, a physical anthropologist at Wright State University in Dayton, Ohio, published a scholarly article on the identification techniques Porter's medical experts used. "As a scientist, I had to be open to the possibility that they were wrong," she says. But in her judgment, this part of the team's work still holds up. For instance, based on microscopically enlarged photos of the corpse's organ tissues, the scientists were correct in identifying kidney failure as a probable cause of death. That diagnosis squares with descriptions of Jones' final illness, as well as with the recurring tropical fever that he contracted in his youth.

And some of Porter's methods, such as superimposing a photo of the cadaver's head over one of the Houdon busts—were ahead of their time. "I've documented that this was the first use of photo-facial superimposition," Rogers says of a technique still widely practiced today. "There's not one misstep in the case," she maintains. "Everything matches."

Yet Porter’s surviving papers, most of which are in the Library of Congress, reveal some disturbing contradictions. For instance, in 1899, before excavations began, he proclaimed: "There is absolute proof that John Paul Jones was buried in a leaden coffin which undoubtedly bears a plate with his name." But in 1911 he told an interviewer: "I really did not expect to find any name plate, certainly not an engraved one, on John Paul Jones’ coffin."

Moreover, Porter appears to have relied, at least partly, on some seriously flawed evidence. While Hart and Biddle questioned the Jones biography that he used, the great naval historian Samuel Eliot Morison later showed it to be little more than a soufflé of "fictions and forgeries." Porter's researchers trusted it on such crucial facts as Jones' physical stature; Morison noted that "the description of Jones himself, especially his height of 5 ft. 7 inches, [was] a pure invention."

As for the weight Rogers accords the Houdon bust, art historians say that no one should assume—as Porter did—that its measurements ought to match those of Jones' actual head. "Sculptors, especially great ones, don't usually obey the actual proportions," says Nicholas Penny, a senior curator of sculpture at the National Gallery of Art and an authority on Houdon. He suggests that even though Houdon was known to take measurements, and sometimes even life masks, of his portrait subjects (a central point in Rogers' argument), it may have been an element of showmanship as much as anything else.

Porter's documentary research, pinpointing the place and circumstances of Jones' burial, has been reconfirmed by later biographers. And Smithsonian physical anthropologist Douglas Owsley, an expert on historic burials, notes that "it isn't common at all" to find 18th-century remains sealed in a lead coffin filled with alcohol: "I can imagine them doing something like that for a very prestigious individual, if they thought they might be transporting him to his original home."

Yet it bears pointing out that a cemetery set aside for foreign Protestants in Paris—which was, after all, Europe's most cosmopolitan capital in the 18th century—could have contained many such individuals. And while Porter, in his written accounts, insisted that his workmen dug and probed for lead coffins so thoroughly that they could not possibly have missed any, there is no independent proof that they did not. Certainly, the fact that the cemetery lay beneath a built-up city block suggests that they could not easily have explored it completely. Moreover, Rogers acknowledges that it is unfortunate that Porter seems to have made no photographs or sketches of important pieces of evidence, such as the supposed monogram on the linen cap.

One last possible means of proof has not been pursued—and perhaps never will be.

In a dingy display case in the U.S. Naval Academy Museum, a stone’s throw from Jones' crypt, sits a gold-framed miniature portrait of the man painted circa 1780 by an admiring Frenchwoman. On its reverse side, surrounding the entwined initials "JPJ," is a plaited brown circlet: a lock of Jones' hair. If the sarcophagus were ever opened, could the DNA of the hair be compared with the DNA of the corpse?

"It's a fascinating thought," says James Cheevers, the museum's senior curator, when I suggest this. Still, he's not optimistic that such testing will come to pass, especially given Jones' status among academy alumni: "I'm sure the superintendent of the Naval Academy wouldn't extend that permission without going to the highest levels of the Navy, and perhaps even beyond, considering the reverence involved."

Nikki Rogers, however, lights up at the suggestion. "I'd love to find out," she says. "But then again, he deserves his rest. He’s been through a lot."