series reasons

These are reasons from every Evangelion episode and movie. Most of the information isn't in order. I really hae to go back and fix that, but you can deal with it for now . . .

Episode I:
1) Rei appears as a mirage in the the beginning. This could have many meanings, like it tell us what kind of person Shinji is. When Shinji met Rei in front of Eva Unit 01 later in the show, he looked at her, as if he'd seen her before. De ja vu = love, and I don't think they put that there for no readon. (Borrowed from Ryan Xavier's Shinji/Rei site)
2) Shinji pilots Evangelion Unit 01 (who has rejected everyone up to now) and uses it to fight the Third Angel just so Rei won't pilot it and get destroyed. We can call Rei the damsel in distress in this scene.

Episode II:
1) We only see Rei one in this episode, and that's when she's on a stretcher. She merely gazes at Shinji, and Shinji gazes back. We all know Rei is a thinking person, questioning her feelings. She could be contemplating why this boy decided to pilot Unit 01 just so she wouldn't die. Remember, she is "expendable".

Episode V:
1) Shinji notices that Rei is always alone. He wonders why, and continues to think about this "girl who has no friends".
2) He gropes over her. Accident or no accident, it's undeniably intamacy.

Episode VI:
1) Shinji burns his hands and leaves permenant marks on them while trying to pull Rei out of the entry plug. After he sees Rei is alright, he breaks down in tears. I don't remember him doing so for anyone else.
2) Rei smiles for Shinji. The firt time in her fourteen years of life she does so for another person. (Gendou doesn't count, he was a parent figure)

Episode IX:
1) Shinji and Asuka have been living in the same apartment, yet Shinji and Rei pull off a perfect synch during the synch training. Many people have said this is because Yui Ikari's soul is within Rei. Wrong. Yui's soul is within Unit 01. The perfect synch between the two could be a sign . . .

Episode XI:
1) As the Eva Pilots are going to Nerv, and when the pilots are climbing the vents, Rei's eyes go to Shinji.
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