Ayanami Rei

Name: Ayanami Rei
Age: 14 years old (born 2001)
Parents: unknown
Rank: 1st child
Evangelion Unit: 00
Notes: no information in files (no past); the original Evangelion pilot; has worked closely with Commander Ikari for several years on the Evangelion project; has some difficulty controlling her Evangelion Unit; appears emotionless and passive to a fault; will obey any order, no matter its consequences; highly devoted to Commander Ikari; no relationships with anyone other than Nerv personel (no personal friends, no real contact with classmates, etc.); no opinions on her fellow pilots

Rei is a quiet girl who very rarely speaks and even more rarely shows any sign of emotion. She has no past; there is nothing about her in Nerv's data files. She is a mystery to everyone but Gendo and Ritsuko, but they won't say who she is nor where she came from. Rei likes to be left alone; she would rather the presence of books to that of people, not because she wants to learn but because people are too loud and emotional. Rei hides her emotions away deep inside her and is nearly mindlessly loyal to Gendo. She sees him as her father, the only person who has ever truly cared for her; when Unit 00 goes berserk with Rei still inside, Gendo has the entrance plug ejected and runs to see if Rei is alright. He opens the blistering-hot metal with his own hands.
Rei has a strange relationship with her Evangelion: once, as she watches from behind the protective glass, Unit 00 goes berserk and begins to hit the glass exactly where Rei is. She does not move, nor show any fear. Finally, just as Unit 00 was about to pierce the glass, the power was cut off.
Shinji envies Rei's relationship with his father. When Shinji insults Gendo, Rei slaps him (one of the few times she shows anger). Rei is the first child, and is often the first one sent into battle. She is the most competent fighter of the three children (possibly because she has had more training and has been through the test stages of the Evangelion Units) and will obey any order given to her. Because of this, she usually ends up badly hurt, with her Eva in pieces.
In one episode, Shinji and Asuka have to learn to work together. They are told to learn a choreography and use it to have their Evas defeat the Angel. We see Misato, Kensuke, Toji, Rei and Hikari (Asuka's friend) watching the two pilots trying to coordinate their moves on two Twister mats. Shinji is actually trying; Asuka falls over and swears. "This is hopeless!" she cries. Misato tells her: "Keep trying." Asuka scowls. "And what if I say I quit? There's no one else to do this!" she says smugly. Misato calmly turns to Rei. "Rei? Would you try, please?" Rei rises and takes Asuka's place on the Twister mat. The music begins and Rei and Shinji begin to move, in perfect syncronization. Eventually, Shinji falls over and Rei wordlessly returns to her seat.

We eventually learn that Rei is a clone: she was made by Gendo and the staff of Gehrin (Nerv's previous name). She was an experiment to see if human DNA and Angel DNA could be combined. The result was a mix of Yui's DNA and Adam's (or Lillith's, I'm not sure which). Rei dies twice in the series, but always comes back. The first time, she is strangled by Naoko when she is only 9 years old (I'm still not sure if there originally was an Ayanami Rei, or if the child was also a clone). The second time, she blows herself and Eva 00 up to save Shinji. Everyone believes she is dead, but then Misato gets a call from the hospital saying that Rei is only badly wounded. Rei doesn't remember having saved Shinji, and quietly murmurs: "I think... I must be the third." Shinji, of course, understands none of this and gradually begins to fear her. She later goes home and unwraps all the bandages, only to find that she hasn't a scratch, despite having been told she was gravely wounded. She picks up Gendo's broken glasses and begins to cry (the 1st Rei never knew how to cry; the 2nd only learned in her last few moments of life). She wonders why she is crying, saying that she's never seen these glasses before, and tries to crush them.
Ritsuko later destroys all the clones except the one currently activated. She does this because she's finally realized that no one can take Rei's (and Yui's) place in Gendo's heart. Also, in another episode, an Angel has defeated Asuka and Shinji has refused to pilot for various reasons. Rei steals a bomb and goes to meet the Angel. Everyone gasps and Gendo anxiously rises from his chair. "Rei!" he cries. She looks grimly determined as she answers: "It's alright. I can be replaced." It is assumed that this is a reference to Shinji, but couldn't it also refer to the clones?
Hundreds of copies of Rei were made; the other clones are at the core of the dummy plug system. They have no souls and no emotions; they are but empty husks, waiting to be filled with a soul. Only when a clone is activated does it have a soul (the Reis in the series do have souls, since they have been activated). While there isn't supposed to be any real differences between the Rei clones, there seems to be a kind of evolution taking place. The 1st Rei was naive and understood nothing of people or of life. The 2nd was completely devoted to Gendo, possibly because she realized Gendo's devotion to her. The 3rd clone has evolved even further: she sees Gendo for what he truly is and realizes that he cares only for Yui. She defies Gendo in the end, and is much more wary of everyone.
The entire story of Eva is based on loneliness, and the loneliest of all is Rei. She is different in body and mind; the person most like her is Kaworu, and she pushes him away. As the 16th Angel tells her: "(Loneliness) is what your mind is. It is what fills your soul!" Rei knows nothing but sorrow and pain; she does not want to be alone, but she does not understand humanity enough to approach it.

The prototype of the Evangelion models, Unit 00 is the first Eva. It seems to be at least slightly aware of its surroundings: it recognizes its pilot and tries to kill her once. Eva 00 looks softer and more feminine than Evas 01, 02 and 03. It is the same blue as Rei's hair, and their profiles look strangely alike.