In 2003, not long after the smoke cleared from allied bombs, U.S. soldiers were combing through the flooded detritus of Saddam’s notorious intelligence ministry in search of weapons of mass destruction. No WMDs were found, of course. But among reams of waterlogged documents, troops wading in water four feet deep spotted Hebrew lettering among the Arabic.

They were the stolen treasures of Iraq’s Jews—including a 16th century Bible, torah scroll fragments, Hebrew school books and handwritten sermons. They were some of the last heirlooms of an ancient community on the cusp of extinction.

More than a decade later, still another chapter is being written. The relics are safely housed in the U.S., but are triggering an international controversy involving such disparate characters as Judith Miller, the former New York Times reporter, and Dr. Ruth, the octogenarian sex therapist. That is because by June, the archive must be returned to Iraq, where their protection cannot be guaranteed and where all of five Jews remain.

“We’ve worked on many different interesting projects, but this one is very special,” said Doris A. Hamburg, the director of preservation programs at the National Archives. She supervised the restoration of the possessions, which include more than 2,700 books and tens of thousands of documents in Hebrew, Arabic and Judeo-Arabic.

Hamburg herself went to Iraq during the post-war frenzy, commencing the document rehabilitation by storing the papers in a rare find in the war-torn desert: a freezer truck. They were then shipped to Archive laboratories in Maryland where mold was removed and rips mended. Hours of painstaking repair later (at millions of dollars in U.S. taxpayer expense), the relics are now on display at the Museum of Jewish Heritage in Lower Manhattan.

That exhibit is scheduled only through mid-May. Safe removal of the relics required a treaty between the Coalition Provisional Authority—America’s temporary viceroys in post-war Iraq—and the fledgling Iraqi Ministry of Culture guaranteeing their eventual repatriation to the Middle East. This, despite what could only be described as fraught security in Iraq—and no arrangements that would satisfy representatives of the artifacts’ original owners.

“There is no Jewish community in Iraq to claim the ownership—only the Jews of Iraq, who live outside Iraq, can claim them,” said Maurice Shohet, president of an organization of Iraqi Jewish exiles. He says Iraqi officials can make no demand on that which was never theirs.

Iraqi officials insist otherwise. Sarhad S. Fatah, a counsellor at Iraq’s United Nations Mission, attended the Museum’s private opening celebration on February 3 (along with Dr. Ruth, another guest). In a brief interview, he told me that any deal would have to involve “retaining the National Archives of Iraq.”

In a statement to the Daily Beast, the ambassador to Washington, Lukman Faily, added “the archive is Iraq’s property,” but added: “We are in discussions with our American counterparts to find a creative approach to access and sharing of these documents.”

A U.S. State Department official, insisting on anonymity, said in an email the Obama administration understands “the sensitivities surrounding these items,” adding discussions are likely to intensify as the visit of the director of Iraq’s National Library and Archive approaches. The date for his trip hasn’t been set.

To some, Iraq’s interest in the artifacts is less about embracing its complicated Jewish history, and more about airbrushing its current ethnic conflicts.

Says Shohet: “The Iraqi government wants to showcase minorities — according to their official declarations—that they have an old Jewish community, very active, it has a culture—and that’s according to the media, and that according to their public information.”

In other words, propaganda.

The Archives have photographed many of the images, posting them online; but like many things, peering at a computer screen pales to witnessing the real thing. The worn threading on prayer books surely isn’t just from water damage; one can easily envision generations holding them in divine supplication: for health, for a spouse, or for a better life for one’s children.

Jewish life between the Tigris and Euphrates is so old that calling it “Jewish” isn’t quite right—perhaps Hebrew or Israelite or Abramaic is a closer fit. God is said to have summoned Abraham from Ur, now in Southern Iraq. Several times, the Jews of Israel were exiled to what is now Iraq, and Babylonia became a center of Jewish scholarship. That relative calm shattered just as millennia of European Jewish life was also unraveling. In 1941, at least 150 Jews were killed in a Baghdad pogrom. The establishment of the State of Israel in 1948 provided ample ruses to claim Jews as a fifth column. Under Saddam’s Baath Party rule, anti-Semitism was often wielded as a diversion from real internal problems. As a result, tens of thousands left.

Such was the case with Shohet, who fled Iraq in 1970, when only 3,100 Jews remained. Otherwise buttoned-down, Shohet, 64, grew moved walking through the museum Monday evening, when he pointed to a prayer book written by a former teacher.

There are many theories about how and when the documents ended up in Saddam’s intelligence ministry, also known as the Mukhabarat. Shohet has one about Saddam’s thugs entering a Jewish center, with an Israeli co-conspirator. He says it dates from 1975, and is based on his discussions with fellow Iraqi Jews. It was unclear why the Israeli was there, but Shohet adds that soon after the raid, the Jewish community was presented with a casket to bury and all but told not to ask questions.

Another theory is given by Harold Rhode, a liaison to the Iraqi opposition amid the U.S. occupation and now a senior fellow at the Gatestone Institute, where former U.N. Ambassador John Bolton is the chairman. In an online post, Rhode suggests the raid happened in 1984, and from a synagogue.

Rhode also writes that he learned of the cache of relics in 2003 from Ahmed Chalabi—the disgraced Iraqi opposition leader, who Rhode says also told Judith Miller of the rare find. (Rhode lists former Vice-President Cheney and former Defense Secretary Rumsfeld among the real heroes, for intervening and assuring the documents were saved).

Rhode writes that Hussein’s men first took the possessions to humiliate the few Jews left. And he argues that humiliation is also at the center of Iraqi insistence the documents be returned—to let them stay in the U.S. would be derided in Iraq as a victory for American and Jews.

In his statement, Faily, the Iraqi ambassador, said that the documents “tell us what humanity can accomplish when we live together in mutual respect….that, together, we can create a world with more museums and fewer Mukhabarats.”

A compromise may yet be reached, to save face on the Iraqi side, while on the other affording a community stripped of almost everything to retain dignity and scraps of their identity.

Baghdad doesn’t quite scream out as a destination for meditative museum-browsing. Doubly unrealistic is the expectation that those searching out exhibits on its vanished Jewish past could view the exhibit with the same peace they now can experience in Manhattan.