Most likely the Romans would have burned the corpses of their enemies, or they would have thrown them into mass graves. Given the arrangement of the burials, it is certainly more plausible that the war victims were neatly buried in the cemetery by Jews. The dating of the ceramics and the regular arrangement of the tombs therefore suggest that we must think of another historical event. One possibility is the Parthian invasion of 40 BC which is very well linked to the damage and traces of a very extensive fire reported by de Vaux at the end of the Hellenistic period Ib. More or less contemporary with this event is also the beginning of the reign of the vengeful King Herod the Great (37 BC – 4 BC). We know from de Vaux’s reports that Khirbet Qumran was most likely never inhabited for the duration of Herod’s reign. It is therefore possible that it was the troops of Herod the Great who massacred the victims contained in the cemetery, at the very beginning of the reign around 37 BC. Assuming the theories of R. Eisenman to be valid, one could think that the Jews have continuously occupied Khirbet Qumran even after the destruction by the Romans in 68 AD. and therefore had the opportunity to bury their victims with dignity, who would have been killed by the Romans.
In 2000 Joe Zias, an archaeologist and anthropologist from the Hebrew University of Jerusalem, in a work that appeared in Dead Sea Discoveries, 7, 2000, pp. 250-53 brought new elements that downsize both the question of the presence of women in the Qumran cemetery and the possibility that the bodies belong to victims of a great massacre. Zias points out in his work the difficulties encountered in determining the sex of the human remains found as well as some inconsistencies. In a 1998 study O. Roher-Ertl, for example, changed the sex assignment of some human remains among those found by de Vaux, who had examined the skeletons before him had become confused. Zias then points out that some of the graves in which female remains were found actually have an east-west alignment quite different from the north-south one characteristic of most graves in the cemetery. According to Zias, there are a number of graves in the Qumran cemetery that have east-west alignment and burial characteristics different from those of the rest of the cemetery: these graves are not related to Khirbet Qumran but could be relatively recent Bedouin remains, buried here according to Islamic practices. Regarding the issue of broken bones found in some remains, Zias considers that this is possible in burials that are more than two thousand years old and is due to the normal process of consuming the bones and settling the ground over many centuries. According to Zias, therefore, the theory of female presence and even that of a massacre would be somewhat reduced.
In the areas surrounding Khirbet Qumran there are the famous eleven caves, numbered from 1Q to 11Q, within which many manuscripts have been found in a fragmentary state, as well as shards of jars and other finds. The set of pieces of scroll that have been found shows that they have been copied over the course of a few centuries, by many different scribes. It is therefore an entire library of scrolls, essentially religious in character, not a few homogeneous scrolls written by some copyists in the space of a few years. The bulk of the documents is therefore attributable not to a single private library but rather to a large community library that has grown over the centuries or to many libraries put together. Figure 2 shows the geographical distribution of the caves in the surrounding area of Khirbet Qumran. The vast majority of manuscripts found in the caves starting from 1947 and in the 1950s are written in Paleo Hebrew, there is also a certain percentage of documents written in Aramaic while in Greek only very few fragments have been found, all relatively very small, concentrated exclusively in two caves, the 4Q and the 7Q.