Lilith, the crucified mother of us all...
Lilith is, quite simply, the mother of both humanity and the other sixteen Angels (yes, INCLUDING Adam). Lilith is also an instrumental being in the plans of Gendo Ikari and SEELE for igniting the Third Impact.
Speaking Biblically, Lilith was the first wife of Adam. Because she was not made of Adam's own body like Eve, she was not completely subservient to him and left him to wander the Earth. Eventually, she met Adam and Eve's son Cain and with him, started the entire human race.
The Lilith seen in Neon Genesis Evangelion originally started out as one almost God-like being who was divided into Lilith and Adam by the First Impact. As Shito, Adam and Lilith became mortal beings within the confines of two regions known as the Black Moon and the White Moon. Lilith's home was the Black Moon, embedded in what would become known as GeoFront, underneath Tokyo-3. In the Black Moon, Lilith produced an egg from which came the angelic being known as Lilim. The Lilim divided continuously until becoming the human race as we know it today. By the Third Impact, the one outlined in the Human Complementation Project, the final evolution of humankind would be to return to being one being devoid of pleasure or pain (the Lilim) and returning to Lilith.
The mortal form of Lilith is a tortured, mangled body crucified on a large red cross deep within Terminal Dogma, at the heart of GeoFront. The legless Lilith bleeds the LCL fluid used in the EVA Units (Shinji is the first to notice this, commenting in the series that the EVA smells of blood). She dons a mask bearing the symbol of SEELE as a means of luring the Angels to Lilith under the impression she's really Adam, in SEELE's hope that an Angel will touch Lilith and set off the Third Impact. Also, Rei Ayanami is a clone of both Lilith and the late Yui Ikari.
The first indication that this being is really Lilith comes in episode 24 of Evangelion, when Kaworu Nagisa realizes what he once thought was Adam is really Lilith and pleads with Shinji to kill him. Though the Third Impact was avoided, in End of Evangelion, Rei III DOES unite with Lilith as a means of betraying Gendo and thus sets the final evolution of mankind into motion.
Evangelion: Death & End of Evangelion © Studio Gainax. Licensed by Manga Entertainment, Inc. All Rights Reserved, or as otherwise directed by Manga Entertainment. Created by Hideaki Anno.