... to the realm from which you were borne.
Recently on a image-board someone asked what this was about:
Look at the older hindu drawings of the chakras and the third eye, the third eye is surrounded by two delicate flower-petals... kinda like a vagina.
Here’s a picture of the third eye, notice the twin petals...
... any similarity to Lilith's mask is totality coincidental... of course.
To tie that up: Shinji is merging into Rei's third eye, where Rei's soul sits, at the centre of her brain. So you got some soul merger going on, I think this has to do with what Rei and Shinji both do in the sea of LCL. They have both merged their souls together during sex, Rei wanted to do this previously but described it as: becoming one with Ikari.
Shinji is becoming one with god‘s (in this case, Rei's) oversoul.
There’s also the obvious symbolism of returning to the womb, to the mother of all things through her (now) fragmented (in us) soul (it won’t be afterwards though, she’ll be complete and her S²/Immortality Drive ringed DNA will fire up and maybe complementation will occur for Lilith as well, who knows) but that stuff shouldn’t really need to be mentioned.
Everyone take a closer look at the opening where the third eye is coming from. Look familiar, (complete with clitorus).
This is one instance where Anno didn't want to leave ANYTHING up to the imagination.
they also appear on GNR's hands
Rei is on top of Shinji, her hands and wrists are inside his chest.
Shinji, still holding Misato's cross is resting his head on Rei's lap.
Rei and Kaworu is standing in front of Shinji.
GNR leans back, her 12 wings wither away
Eva-01 (Yui) busts out of GNR's eye.
GNR's hand, still on either side of the black moon, has slits that look a LOT like...
They slits start closing.
Another thing, is the Manga release (which looks like its blurry and taken from a VHS source or something) it's a lot harder to tell. The renewal release looks a LOT better.