Prologue
"What do you choose, Shinji?"
Shinji looked up at Rei. He was curled up beside her, with his head resting in her lap as she stroked his hair. He looked away again and watched the orange lights signifying peoples souls float off in the distance. It was all over now. Everyone's souls had been joined together. There was no longer any place for anger, fear, or sadness. Joined into one being, all that humanity felt now was content.
But Shinji, he was not content. Something, something just felt wrong being one with all of humanity. Though he was one with everybody, he wasn't able to interact with them. True, he could meld with others, becoming one, sharing memories, but there was nothing physical. He felt as if everything happening now was all an illusion. This was not the real world. Despite the fact that he was one with all of humanity, he felt more alone here than he had ever been before.
Shinji turned his head again and looked up at Rei. Her crimson eyes stared down at him, set into a beautiful face framed by her blue hair. She was smiling down at him faintly, and he felt his heart beat quicken, helped along by the fact that she was completely nude. Her perfectly round breasts, and the rest of her glistening, pale, and flawless skin; it was all right in front of him. He tried not to think about that too much. He was naked as well, after all.
He knew that she was a partial clone from his mother now, but that didn't stop him from thinking that she was the most beautiful person that he had ever seen. Not even learning that she had also been an Angel, one of the supposed "enemies" of mankind, had been able to change his mind about that.
Back before all this happened, before SEELE and his father had forced Third Impact to occur, Shinji had often wished that one day, when all the fighting was over, that he just might have the courage to ask Rei out. Several times, he had even dreamed of marrying her someday. It had been one of the few things that Shinji had truly wanted. It had nearly drove him insane when he watched Rei's Evangelion unit self-destruct to save him, and then when he learned that she really had died, and was replaced by a clone…
But none of that mattered now, Shinji thought as he turned away from Rei again. With the way things were, Shinji would never be able to be with Rei the way he had wanted. Everyone would always be there, next to him, beside him, in him; crammed into one being against their will.
That was when Shinji realized it. It wasn't that humanity didn't feel anger, pain, or sadness hear, but instead they couldn't. It wasn't that being one with everyone made humanity feel content, but that their ability to feel emotions had been taken away from them, and now being content was the only emotion they could feel. They were human no longer.
Shinji swallowed, realizing that he could still feel emotions, though they had been dulled, and yet he somehow knew that everyone else couldn't feel anything at all. He turned to look up at Rei, who was still looking down at him, smiling.
She was doing it.
Shinji could feel it, now that he realized what was happening. He had not yet become one with the rest of humanity. She was still holding him back from everyone else, keeping him with her.
"Which do you choose, Shinji?" she asked again. "Do you want to become one with humanity? Or do you want everyone to be separated once again?"
She was holding him back, giving him the choice, putting the fate of humanity in his hands.
"Why?" Shinji asked.
Rei cocked her head slightly. "Why what?"
"Why me?" Shinji asked. "Why did you choose me?"
Rei stroked his hair, and smiled. "I felt you calling to me, Shinji. I could feel how much pain you were in, and I wanted more than anything to save you from it. In the billions of eons that I have lived, I have never wanted to save anybody more than you."
"Eons?" Shinji asked.
Rei nodded, and looked out at the floating lights. "You know that I am an Angel. It was my soul that lived in the body you knew as Rei Ayanami. My real name is Lilith, and I have existed since before the universe began. My memories were repressed until I rejoined with my true body when your father attempted to use me to control Third Impact himself. But even before I regained my memories, I wanted to save you. I cannot explain it, but as I watched you through the eyes of Rei Ayanami, you slowly became the most important thing in the universe to me both as Rei and as Lilith." She looked back down at Shinji. "So Shinji, which do you choose?"
Shinji looked up at her for a moment, trying to comprehend what she had told him. He knew somehow that even though she was a different person, she was still the Rei he had known, and she had given him the power to decide humanities fate.
"If I wanted everyone to be separate once again, would everyone come back?" he asked.
Rei--Lilith--shook her head. "Only those who have the will to return to their bodies will be able to raise the walls of their souls once again. Many people will not be able to return; some of them are people you know."
Shinji swallowed, and sat up, lifting his head from Lilith's lap, and thought for a moment. Then he turned and looked back at her. "And what about you? What will happen to you?"
Lilith smiled sadly back at him. "I will die."
Shinji's eyes widened, as he felt panic starting to break though the cushion that was dulling his emotions. He didn't want her to die. She was still Rei, he couldn't condemn her to death!
Seeing the distress in his eyes, Lilith reached out a hand and cupped the side of his face. "Don't worry," she said, trying to comfort him. "I have lived long enough, it's alright."
"Why do you always do that?" Shinji asked, brushing her hand away and turning away from Lilith as he felt tears beginning to form in his eyes.
Lilith faltered. "Do what?" she asked, frozen.
"You always act like your life isn't important. You are always willing to through your life away. Your life is more important than that!"
Though Shinji couldn't see it, Lilith smiled and scooted closer to him. She wrapped her arms around Shinji from behind, pressing her bare bosom to his back and resting her head on his shoulder. Shinji froze.
"It has always made me happy to hear you say that, even when I was only Rei Ayanami." She tightened her grip on him. "I don't want to die. I want to be with you Shinji, but I know you could never be happy here in this place. My death is the only way."
Shinji felt a tear drop onto his bared legs. He squeezed his eyes shut. He didn't want to have to condemn Lilith to death. He just couldn't!
Slowly, Shinji detangled himself from Rei's arms, and turned around to face her, looking determined. "I already failed to save you once before," he said, the memory of Unit Zero exploding from the inside out all to clear. "I don't want to make that same mistake again."
Lilith looked thoughtfully at Shinji. "Perhaps there is one other way," she said slowly.
"Really?" Shinji said quickly, eyes wide. "Whatever it is, I'll do it! I need to!"
"Shh," she said, hushing Shinji, and regarded him with searching eyes. "This will not be an easy task, and once you have started it, I will not be able to help you. You will have to relive some of the most painful moments in your life."
Shinji nervously looked downwards. I mustn't run away, he thought. I'm always telling myself that. This time, it's more important than ever. His eyes flickered up at Rei for a moment, before returning to the ground. I can't lose her like last time. He looked up again. "If I do this, everything will be back to the way it was?"
Lilith nodded. "It will be as if Third Impact had never happened."
Shinji took a deep breath, and then said, "I'll do it."
Lilith nodded her head in ascent, and then crawled forward and kissed Shinji on the lips. She pulled away, smiling, a second later, leaving a stunned Shinji staring wide-eyed at her.
"Say hello to Rei for me," she said, smiling sadly.
And white light enveloped everything.
"Were sorry. Due to the stay of special emergency, no lines are currently available. This is a recording."
Shinji pulled the green pay phone away from his ear and placed it back into its cradle in the booth in front of him. The he stared at the hand that had held the phone only seconds before, and he began to clench and unclench his head repeatedly. Turning away from his hand, he looked up at the tall skyscrapers that made up the majority of Tokyo-3.
Everything was eerily still and silent, and then Shinji let out a whisper so quiet that not even he could really hear it, but he still knew undoubtedly what he had said.
"I'm back."