An image of the scrolls during the opening.
The Dead Sea Scrolls is the in-universe name for the Secret Dead Sea Scrolls, a set of documents that serve as the primary guide and philosophy of SEELE. Little is known about the Dead Sea Scrolls from the series, except for what SEELE alludes to during their meetings and what is stated in the Classified Information section of the Neon Genesis Evangelion 2 video game.
In Evangelion
It is known that the Scrolls are of extraterrestrial origin and that they serve as a manual on the use and purposes of the contents of Black and White Moons; a Seed of Life and the Spear of Longinus.[1] They detail rules on how to use these items, and are often referred to as a prophecy of sorts; right down to the extent of the order and times of release or arrival of the Angels.
SEELE possessed vast wealth and power, and being founded originally as a religious organisation they funded investigations into relics of their faith. This culminated with the excavation of the Secret Dead Sea Scrolls. Upon discovery they were taken to their headquarters. The irrelevant discoveries were released to the public as the Dead Sea Scrolls, while the the Secret Dead Sea Scrolls were kept by SEELE. They would later be used to put their ultimate plans of a Second and Third Impact, followed by Instrumentality into fruition.
According to Gendo, the Dead Sea Scrolls do not tell everything.
In Rebuild of Evangelion
It appears in Rebuild the Dead Sea Scrolls are similar to those in Neon Genesis Evangelion.
In Reality
The real Dead Sea Scrolls were discovered in eleven caves at Qumran in 1947 on the northwestern shore of the Dead Sea. The texts are mostly fragmented, with the exception of a few relatively intact scripts. Scripts and script fragments are numbered according to the cave they were found in. A number of scrolls are in Hebrew, while others are in the Aramaic language. Fragments of every book of the Old Testament, except for the book of Esther, have been found among the Dead Sea Scrolls.[2]
A number of Dead Sea Scrolls had not been made available to the public at the time of the series' production which have since been released, and the mystery surrounding their contents has disappeared.[3]