The recent decoding of a cryptic cup, the excavation of ancient Jerusalem tunnels, and other archaeological detective work may help solve one of the great biblical mysteries: Who wrote the Dead Sea Scrolls?

The new clues hint that the scrolls, which include some of the oldest known biblical documents, may have been the textual treasures of several groups, hidden away during wartime—and may even be "the great treasure from the Jerusalem Temple," which held the Ark of the Covenant, according to the Bible.

The Dead Sea Scrolls were discovered more than 60 years ago in seaside caves near an ancient settlement called Qumran. The conventional wisdom is that a breakaway Jewish sect called the Essenes—thought to have occupied Qumran during the first centuries B.C. and A.D.—wrote all the parchment and papyrus scrolls.

But new research suggests many of the Dead Sea Scrolls originated elsewhere and were written by multiple Jewish groups, some fleeing the circa-A.D. 70 Roman siege that destroyed the legendary Temple in Jerusalem.

"Jews wrote the Scrolls, but it may not have been just one specific group. It could have been groups of different Jews," said Robert Cargill, an archaeologist who appears in the documentary Writing the Dead Sea Scrolls, which airs Tuesday at 9 p.m. ET/PT on the National Geographic Channel. (The National Geographic Channel is part-owned by the National Geographic Society, which owns National Geographic News.)

The new view is by no means the consensus, however, among Dead Sea Scrolls scholars.

"I have a feeling it's going to be very disputed," said Lawrence Schiffman, a professor of Hebrew and Judaic Studies at New York University (NYU).

Dead Sea Scrolls Written by Ritual Bathers?

In 1953, a French archaeologist and Catholic priest named Roland de Vaux led an international team to study the mostly Hebrew scrolls, which a Bedouin shepherd had discovered in 1947.

De Vaux concluded that the scrolls' authors had lived in Qumran, because the 11 scroll caves are close to the site.

Ancient Jewish historians had noted the presence of Essenes in the Dead Sea region, and de Vaux argued Qumran was one of their communities after his team uncovered numerous remains of pools that he believed to be Jewish ritual baths.

His theory appeared to be supported by the Dead Sea Scrolls themselves, some of which contained guidelines for communal living that matched ancient descriptions of Essene customs.

"The scrolls describe communal dining and ritual bathing instructions consistent with Qumran's archaeology," explained Cargill, of the University of California, Los Angeles (UCLA).

Dead Sea Scrolls: "Great Treasure From the Temple"?

Recent findings by Yuval Peleg, an archaeologist who has excavated Qumran for 16 years, are challenging long-held notions of who wrote the Dead Sea Scrolls.

Artifacts discovered by Peleg's team during their excavations suggest Qumran once served as an ancient pottery factory. The supposed baths may have actually been pools to capture and separate clay.

And on Jerusalem's Mount Zion, archaeologists recently discovered and deciphered a two-thousand-year-old cup with the phrase "Lord, I have returned" inscribed on its sides in a cryptic code similar to one used in some of the Dead Sea Scrolls.

To some experts, the code suggests that religious leaders from Jerusalem authored at least some of the scrolls.

"Priests may have used cryptic texts to encode certain texts from nonpriestly readers," Cargill told National Geographic News.

According to an emerging theory, the Essenes may have actually been Jerusalem Temple priests who went into self-imposed exile in the second century B.C., after kings unlawfully assumed the role of high priest.

This group of rebel priests may have escaped to Qumran to worship God in their own way. While there, they may have written some of the texts that would come to be known as the Dead Sea Scrolls.

The Essenes may not have abandoned all of their old ways at Qumran, however, and writing in code may have been one of the practices they preserved.

It's possible too that some of the scrolls weren't written at Qumran but were instead spirited away from the Temple for safekeeping, Cargill said.

"I think it dramatically changes our understanding of the Dead Sea Scrolls if we see them as documents produced by priests," he says in the new documentary.

"Gone is the Ark of the Covenant. We're never going to find Noah's Ark, the Holy Grail. These things, we're never going to see," he added. "But we just may very well have documents from the Temple in Jerusalem. It would be the great treasure from the Jerusalem Temple."

(Also see "King Herod's Tomb Unearthed Near Jerusalem, Expert Says.")

Many modern archaeologists such as Cargill believe the Essenes authored some, but not all, of the Dead Sea Scrolls.

Recent archeological evidence suggests disparate Jewish groups may have passed by Qumran around A.D. 70, during the Roman siege of Jerusalem, which destroyed the Temple and much of the rest of the city.

A team led by Israeli archaeologist Ronnie Reich recently discovered ancient sewers beneath Jerusalem. In those sewers they found artifacts—including pottery and coins—that they dated to the time of the siege. (Related: "Underground Tunnels Found in Israel Used In Ancient Jewish Revolt.")

The finds suggest that the sewers may have been used as escape routes by Jews, some of whom may have been smuggling out cherished religious scrolls, according to Writing the Dead Sea Scrolls.

Importantly, the sewers lead to the Valley of Kidron. From there it's only a short distance to the Dead Sea—and Qumran.

The jars in which the scrolls were found may provide additional evidence that the Dead Sea Scrolls are a collection of disparate sects' texts.

Jan Gunneweg of Hebrew University in Jerusalem performed chemical analysis on vessel fragments from the Qumran-area caves.

"We take a piece of ceramic, we grind it, we send it to a nuclear reactor, where it's bombarded with neutrons, then we can measure the chemical fingerprint of the clay of which the pottery was made," Gunneweg says in the documentary.

"Since there is no clay on Earth with the exact chemical composition—it is like DNA—you can point to a specific area and say this pottery was made here, that pottery was made over here."

Gunneweg's conclusion: Only half of the pottery that held the Dead Sea Scrolls is local to Qumran.

Scroll Theory "Rejected by Everyone"

Not everyone agrees with the idea that Dead Sea Scrolls may hail from beyond Qumran.

"I don't buy it," said NYU's Schiffman, who added that the idea of the scrolls being written by multiple Jewish groups from Jerusalem has been around since the 1950s.

"The Jerusalem theory has been rejected by virtually everyone in the field," he said.

"The notion that someone brought a bunch of scrolls together from some other location and deposited them in a cave is very, very unlikely," Schiffman added.

"The reason is that most of the [the scrolls] fit a coherent theme and hang together.

"If the scrolls were brought from some other place, presumably by some other groups of Jews, you would expect to find items that fit the ideologies of groups that are in disagreement with [the Essenes]. And it's not there," said Schiffman, who dismisses interpretations that link some Dead Sea Scroll writings to groups such as the Zealots.

UCLA's Cargill agrees with Schiffman that the Dead Sea Scrolls show "a tremendous amount of congruence of ideology, messianic expectation, interpretation of scripture, [Jewish law] interpretation, and calendrical dates.

"At the same time," Cargill said, "it is difficult to explain some of the ideological diversity present within some of the scrolls if one argues that all of the scrolls were composed by a single sectarian group at Qumran."

Caves Were for Temporary Scroll Storage?

If Cargill and others are correct, it would mean that what modern scholars call the Dead Sea Scrolls are not wholly the work of isolated scribes.

Instead they may be the unrecovered treasures of terrified Jews who did not—or could not—return to reclaim what they entrusted to the desert for safekeeping.

"Whoever wrote them, the scrolls were considered scripture by their owners, and much care was taken to ensure their survival," Cargill said.

"Essenes or not, the Dead Sea Scrolls give us a rare glimpse into the vast diversity of Judaism—or Judaisms—in the first century."