As you all know Rei is the center and source of the dummy plug. She is also a key element in the HIP, how for sure I really don't know why...but I have my theories. Now here's a good question, Ritsuko said that these are all the different parts for Rei (when she took Shinji and Misato into the Central Dogma) now does this mean that Rei is just pieced back together or is she re-cloned? I mean do they just slap on a missing leg and arm, remember after Rei II blows herself up to save Shinji, and they go to salvage the plug, Ritsuko tells one of the clean up crew members to dispose of all the uneccessary parts and keep the ones they can save, or maybe she just said that in terms of dispose the body and clean it up...or do they just re-clone her...or maybe they just take out one of those bodies and transfer her soul into it...ahh. Anyway back to the whole dummy plug thing. People often question what it is exactly, I have come to the conclusion that it's just a way to fake a soul in an Eva unit, almost like an auto-pilot system. Eva's need people inside to pilot because people have souls, well the term "dummy" can be refferred to as fake, so it's a fake plug to fool the Eva into thinking that there's someone inside. Why is Rei the core of the dummy plug? Well, because she has a fake and artificial soul, which is made up of water and light. Hey I just answered my own question.
Theory (before End of Eva)
I think Rei is an angel. Well, first of all she was able to fold an AT field without an Eva to protect Shinji from Unit-02
when he was battling Kaoru..remember the third mysterious AT field? And that reference to Rei standing above all
of them in theTerminal Dogma? Also My other reason...when she meets up with Kaoru, Kaoru tells her,
"You are the same as me." And they both have red eyes. I also think that Rei is a clone
of Yui after she was dissolved into unit-01. Which help back up my Rei being an angel. Hmmm, what do you think?
Fact
She is an ANGEL!!!
For more info go here.
Theory
Gendou knew about the Dead Sea Scrolls, he knew the whole plan. He even knew about the missing pieces (ep. 9 I believe) Anyway, he created Rei to counteract Kaoru, so maybe Rei is the 17th angel
just like Kaoru was. Kaoru was to be the one to initiate the 3rd but he was stopped by Shinji. So in a sense the 17th Angel did start the 3rd. Which was Rei. "You are the same as me."
Reader Theories:
Rei is NOT an angel.
She is something like an angel, ie. AT Field
Rei has an artificial soul, created by Gendo.
Rei pilots Unit 00.
Rei is Rei.
-Peter Svensson