The excavations at Qumran were renewed in 1993, almost half a century after de Vaux had began the original excavations, and continued intermittently until 2004. The recent excavations were conducted under the direction of Yitzhak Magen and Yuval Peleg, on behalf of the Staff Officer for Archaeology in the Civil Administration of Judea and Samaria. The new excavations uncovered numerous finds. These finds enable us to reconstruct the history of the site, from its beginnings in the Iron Age to its destruction in 68 CE:

Phase I: Iron Age (seventh-sixth centuries BCE).
Phase II: from the late second century BCE to the Roman conquest in 63 BCE.
Phase III: from the Roman conquest to the earthquake in 31 BCE.
Phase IV: from the earthquake in 31 BCE to the destruction of the site in 68 CE.

Qumran and the Scrolls:
None of the scrolls discovered in the Qumran area were found at the site itself, but rather in the nearby caves, some at a distance of one km from the site. If we are correct in assuming that the site first served as a military fortress, and afterwards as a center for the production of pottery and date honey, the question arises: where did the scrolls come from, and who brought them to the caves? We maintain that these scrolls had no connection with the site, and they were brought by refugees who had fled during the Jewish revolt against the Romans, from different settlements in Benjamin and Judah, and possibly from Jerusalem, as well. These exiles brought their books with them in their flight, moving along the trails that led south and east from Jerusalem toward the Judean Desert. Many of them arrived at Qumran where, lacking a land route to continue their flight southward, they buried the scrolls in the caves around the site, before continuing their journey by boat on the Dead Sea. It seems that other refugees came with their books to Masada, which would explain the presence of the scrolls at this site, as well.