This seems familiar... or not.
The mass-produced EVAs form a ring about giant naked winged Rei/Lilith and pierce themselves with their lances. A third eye appears on the forehead of Lilith and it is pierced by the Spear of Longinus which is now in the shape of a cross. Rei appears to everyone in the world and cause them to dissolve in LCL. Each member of NERV and everyone on Earth dissolve into LCL after meeting Rei who transforms into a person they desired. The souls of people around the world form into a vertex and is collected into the Black Moon held by Lilith. The only exception to this is Gendo who is still lying on ground mortally wounded in Terminal Dogma. Yui appears before Gendo and states that things are not over even if Gendo dies because Shinji will create a new future. Gendo is convinced and dies at peace and Yui disappears.
Meanwhile, Shinji witnesses all of his memories, sees the souls of people and hears their sentiments before ending up in a vast open space lying on a liquid surface and with Rei sitting on top of him. Rei explains that they are at the LCL Sea, the domain where life originated. It's a world without AT fields, without shape and where one can exist everywhere and nowhere. Rei states that this is world that Shinji had wished for, a world without sadness, hunger, conflict, pain all of the negative aspects of life. Shinji answers that he may have wanted this at one point, but now he rather go back to the previous world because in this new world, there is no one else, no happiness, no feelings and thus there is no difference from being dead. Shinji realizes that going back to the world with AT fields and individuals means that he may get hurt and hurt others again, but he's okay with that and he wants to be able to hold Rei's hand again. Rei and Shinji stand up and they hold hands.
Back in the material world, Lilith loses her wings and spews a stream of LCL from a wound on her neck. As Lilith falls backwards, EVA Unit-01 emerges from her left pupil.
The manga offers a somewhat different depiction of the events of End of Evangelion, but overall results appear to be heading the same way. I don't remember the movie that well anymore, but the difference is that Asuka did not get torn up from the battle with the mass produced EVAs and she plays less of role during the Third Impace. Gendo's death is also entirely different in the manga, and there are multitude of other small details which differ. At the ends though, we still have everyone dissolving into LCL, Shinji ending up at the LCL sea with Rei with the fate of the world in his hands, and he ends up rejecting Instrumentality. The next chapter will supposedly come out in April (May issue), and we'll see if the manga will continue onto the same ending as the movie.