Chapter 1 - The End is the Beginning

"What do you wish for?" These were the words spoken out by Rei to Shinji in the midst of the human instrumentality. She suggestively laid on top of him while they were both floating in a pool of LCL. It was weird but him having to choose what will happen to humanity by this one question was even weirder.

Every choice he made up until here now only made him suffer worse. How could Shinji himself know what he'd wish for.

"I..." He couldn't find the words to make his wish.

Just one slip up and we're all doomed again. Those were the thoughts that were repeating inside his head. What if I make a mistake again. Why do I have to choose? His soul was at a fight with himself but he knew he had to answer now for the sake of him and everyone else he cared for.

"...I wish to see you and everyone again. My life had some downs but without my friends and comrades I don't want to live anymore. Give humanity another chance to live their individual lives without the constant fear of world destruction." Shinji said in a calm but determined voice.

"Why me?" Rei asked, while lovingly laying her hand in Shinji's face "I'm nothing but a mere replica of your mother with some angel dna spliced in. You and the others don't need me in this world."

"I need you. You're neither my mother nor an angel. You're Rei Ayanami. I want to see you smile again." Shinji wished for as he embraced this soft hand he liked so much.

Of course there was a time when Shinji couldn't bear the fact that his mother and Ayanami looked so close to eachother but at this point he had realised that whatever he feels for Ayanami he cannot change it. Without her he'd still be all alone and she's one the reasons why he wants humanity to get another chance at life. There still were things he didn't know about her and the feeling he got from spending all this time with this one girl, made his heart feel warmer.

Rei's face changed slightly. She didn't look as worried as before but Shinji still wasn't sure what she was thinking at the moment.

"You will get hurt again." Ayanami said calmly.

"That's okay." Shinji proclaimed.

"You will suffer through hardships again." Ayanami responded in that same monotone voice.

"That's okay." Shinji proclaimed again. "You can't get the good without the bad. As long as there is a way for us to be happy I can go on with my life...Thank you, Ayanami. I hope we'll see each other again."

"Me too." Rei expressed with a slightly hurt face.

Suddenly everything around Shinji turned white. Ayanami wasn't there anymore and he asked himself if his wish did become true.

Would the world now reset? Would everyone know who he is? Would he get the chance to see Ayanami, Asuka, Misato and his friends again? What if Rei lied to him? What if he was the only one that came to this world. All alone. Forever. These were all questions Shinji asked himself.

"I don't want to be alone anymore. I don't want to be alone anymore. I don't want to be alone anymore. I don't want to be alone anymore. I don't want to be alone anymore." He repeated while waiting for something to happen.

"AYANAMI!" Shinji desperately screamed at the top of his lungs.

Darkness.

Author's notes: So this was the first chapter to my first fanfiction ever. Hope you guys liked it. I tried my best to stay as true to the characters as possible but you never know how true you stay until someone points it out. The romance between Shinji and Rei will be emphasized in this story and you'll get to see how they interact with each other in this new world they will inhabit. There will also be lemon. I would also like to note that English is only my second language so excuse me if I've made some horrible grammar mistakes.