DISCLAIMER: I don't own any of the characters from Evangelion, all these characters are owned Gainax and Hideaki Anno
ALSO: This story is not meant to put down anyone who ships Rei and Shinji, this is merely my story, and is not meant to influence the way anyone thinks
Chapter 1: Take Care
Ritsuko looked at Misato, who had a shocked expression on her face. "So you understand now, why they should know." Said the blonde.
"Yeah, I'm just shocked to know that their DNA is that close, I'd at least expect them to be siblings, but not mother and son," Misato replied "I've always felt like the big sister in his life, and that I should be there for him, but to know that Rei is technically his mother. It's just… Odd to put it lightly."
Shinji and Rei sat next to each other, they had been called into Misato's office for unknown reasons, and Shinji was feeling nervous sitting next to Rei for so long.
"Why did they send us down here," Shinji thought to himself "Misato knows how odd I feel around her. Oh jeez, she probably did this on purpose." Shinji jumped when the door opened, and Misato and Ritsuko walked in.
Misato sat down behind her desk, while Ritsuko stood next to her, the scientist chuckled at how much they resembled Gendo and Fuyutsuki.
Sensing Shinji's nervousness Misato spoke, "Don't worry you too, you're not in trouble. We just have something extremely… Hmm… Important to tell you. Ritsuko do you want to explain it to them?"
"Of course. Rei. Shinji. You two are related. We at first thought it was simply a brother and sister type deal, but now we see; well, how do I put this. You two are more close to mother and son, than brother and sister.
Rei's mouth opened slightly, and Shinji bowed his head and held his head while this info hit them both. Sensing the tenseness of the situation, Misato spoke "Shinji, if you don't mind, we'd like to speak with Rei in private." Shinji merely nodded his head slightly, and walked out.
When Shinji left, Misato walked over to Rei, and in a pure act of consoling, grabbed Rei's hands. "Rei," she started "Ritsuko and I have decided to let you choose what you would want to be to Shinji. We can't simply tell you to act like you're not related, that would be wrong, and would just lead to more problems. So Rei, what do you want to be to Shinji? Would you like for him to consider you as a mother, or a sister?"
"What would that mean to me," Rei thought "I am merely an extension of his mother, so perhaps that would give me a purpose beyond piloting the Eva." She looked at Misato and finally spoke, "I believe it would be beneficial for me and Ikari to be mother and son."