Jones had a storied career. He died in France. It took many years to find his body and bring him back to the United States:
In 1905, Jones's remains were identified by U.S. Ambassador to France Gen. Horace Porter, who had searched for six years to track down the body using faulty copies of Jones's burial record. Thanks to the kind donation of a French admirer, Pierrot Francois Simmoneau, who had donated over 460 francs, Jones's body was preserved in alcohol and interred in a lead coffin "in the event that should the United States decide to claim his remains, they might more easily be identified." Porter knew what to look for in his search. With the aid of an old map of Paris, Porter's team, which included anthropologist Louis Capitan, identified the site of the former St. Louis Cemetery for Alien Protestants. Sounding probes were used to search for lead coffins and five coffins were ultimately exhumed. The third, unearthed on April 7, 1905, was later identified by a meticulous post-mortem examination by Doctors Capitan and Georges Papillault as being that of Jones. The autopsy confirmed the original listing of cause of death. The face was later compared to a bust by Jean-Antoine Houdon.
Jones's body was ceremonially removed from interment in a Parisian charnel house and brought to the United States aboard the USS Brooklyn, escorted by three other cruisers. On approaching the American coastline, seven U.S. Navy battleships joined the procession escorting Jones's body back to America. On April 24, 1906, Jones's coffin was installed in Bancroft Hall at the United States Naval Academy, Annapolis, Maryland, following a ceremony in Dahlgren Hall, presided over by President Theodore Roosevelt who gave a lengthy tributary speech. On January 26, 1913, the Captain's remains were finally re-interred in a magnificent bronze and marble sarcophagus at the Naval Academy Chapel in Annapolis.