Warning Spoilers!

UPDATE Alright now here is somewhat of a detailed event of what happened. Rei denies Gendou entry into Lilith. Turns out Rei ditches Gendou to go to Shinji (She hears him screaming when he gets carried away by Eva Units 5-13, so she does care!). She flies up and they (Rei and Lilith) merge. Lilith's mask falls off (so it wasn't really her face, it's all blank), and eventually Rei's body takes shape, and Rei's face takes over the blank but there are no eyes. Lilith/Rei grabs Unit-01. Units 5-13 make facial rei like facial expressions. Then a big naked Kaoru detatches from Lilith/Rei and grabs ahold of Unit-01. The Lance that was near Unit-01 finally pierced through and merged with Unit-01. A red cross (like Lilith's) emerges and Unit-01's body is covered with tiny eyes (like the one on the spider angel). Fuyutsuki then makes a statement:

The seed of the tree of life which angels have, and the seed of wisdom which a person has. Eva Unit-01 had both things, in which her existence became equal to God. Then, she was reduced to the tree which is enough for the large river of the life. When the 3rd impact began, our future was entrusted to Ikari's son whether it become the ark which saves a person from nothing or it become the devil who ruined a person.
This explains why Unit-01 and Shinji are so important.

Anyway this is where it gets crazy. It becomes this huge montage of self reflection and actualization among the characters. Like eps. 25 and 26 of the TV series, only much cooler. Well the whole idea is that all the elements of reality are becoming somewhat of a dream like state.

We then see the stuff that's happening outside of Lilith/Rei. Lilith/Rei, Unit-01 through 13 are all ascending higher into the sky. Lilith/Rei who is pracrically the size of the world picks up the Geo Front and spreads her wings. Her face is sad, maybe because the humans that she bore have rejected her. You get this idea after Rei says, "The world is full of sorrow. People are enveloped by emptiness." Then everything begins to dizzolve into LCL.

Before some of the people dizzolve an apparition of Rei appears beside them. She's dressed in her School uniform. Wait a minute. Didn't we see something like this in the first episode? Hmmm...was the whole thing, a dream?

Anyway the scene shows Gendou lying on his back with an apparition of Yui.

Gendou : I have waited for the day that I may meet you again Yui. I only hurt Shinji when I was near him. That's why I did nothing for him.

Yui : You were afraid of Shinji weren't you?

Gendou : I don't believe anyone has loved me. I don't deserve to be loved.

Mysteriously an apparition of Kaoru in his student uniform stands by Gendou.

Kaoru : You're just running away. You reject the world before you get hurt..

Yui : You're afraid of the things within a person that can't be seen with the naked eye.

Then an apparition of Rei in her uniform stands next to Gendou.

Rei : You closed off your heart because you were afraid.

Unit-01picks up Gendou.

Gendou :This is what I deserve. I'm sorry, Shinji.

Unit-01 devours the upper half of Gendou.

Reader Theories:

• Asuka patting Shinji's cheek could be showing that she has improved. If Shinji had did the strangling bit earlier in the show,Asuka would of yelled "BAKA SHINJI!" and knocked him across the room. But with the cheek pat, it seems she is saying.."Oh Shinji! Your Still Acting like that?"
  -Robert Geiger