In their book, The Dead Sea Scrolls Deception, Michael Baigent and Richard Leigh support the view of a Catholic conspiracy.
"They claimed to have uncovered the sensational story behind the religious scandal of the century," says Professor Timothy Lim, a Dead Sea Scroll expert.
"It was alleged there was a conspiracy, in the form of a modern inquisition led by Joseph Ratzinger, to suppress unpublished Qumran scrolls that might be 'harmful to Church doctrine'.
"And then, when all the scrolls were open to the world, we found there was none of the damaging information they claimed there would be. Of course, the conspiracy argument goes that the Vatican had already destroyed it."
But if there were revelations the Catholic church feared, there were others that the entire body of faith would find hard to swallow.
The late John Marco Allegro, the first British representative on original team of academics deciphering the documents, believed they proved that Christianity had grown from a cult that drew its faith from hallucinogenic mushrooms.
He was convinced that Jesus Christ never existed but was an analogy for the Fly Agaric mushroom, around which the activities of an ancient fertility cult revolved.
Another theory, apparently supported by the Scrolls, was that early Christianity was a political movement, transformed by St Paul into the peace-loving religion we know today because he was a Roman spy trying to defuse a potential revolution.
Other scholars believed they asserted there had been another Messiah who died only a few years before Jesus, calling into question his uniqueness. Another school of thought claims the scrolls were actually written by a long lost community of Chinese Jews.
Most scholars, however, are convinced there is actually no mention of Jesus in the them at all.
The Scrolls, written on animal skins, papyrus and, in one case, copper, were stored away in pottery urns in the caves by their authors, members of the austere Essene sect who lived in a nearby celibate all-male religious community. "Once a scroll was worn out they didn't destroy it because the name of God was on it. Instead it was stored away," says Professor Lim of Edinburgh University.
Among the most fascinating finds was the kind of treasure list Indiana Jones would kill to get his hands on.
Etched on the copper scroll are the locations of 64 hiding places of hoards of gold and silver, supposedly hidden throughout the region and which today would be worth billions.
Attempts have been made to track down the riches but - as far as anyone is willing to admit - with no success.