Well, this is it. The last chapter to my second (and possibly last) Evangelion fanfic. Hopefully, I satisfied the peoples' lust for a good post-ending to End of Evangelion, and I would like to thank all those who reviewed my story, and a special thanks to CyberForte for helping me get this story together.

Also, concerning credit where credit is due, the three psychoanalysis chapters where Omega penetrates the pilots' minds are to be attributed entirely to CyberForte. Also, I have posted a modified disclaimer to make sure NOBODY steals my stuff. So, please, read and enjoy the last chapter of The New Beginning.

Modified Disclaimer: I do not own Neon Genesis Evangelion or the First Ancestral Race, as those belong to Hideki Anno and GAINAX; however, I do own Alpha Omega, Alpha Omicron, Delta Theta, the terms Nightfire and Nufire, the followers of Delta Theta, and any or all planets, stars and vessels that belong to my version of the First Ancestral Race.

EPISODE 34: THE SECOND GENESIS

As Shinji slowly began to open his eyes, he detected a bright light, one that was in fact nearly blinding him. He imagined at first that it was the new darkened violet moon, but when he looked, his expression transmuted to one of amazement in the light of the revitalized yellow sun that stood in the moon's place. Beyond that, once he managed to move his upper torso up, he bore witness to a sight even more astounding.

He saw a rejuvenated landscape, lush and green; the air was warm and the world seemed alive once more. The grave markers he had painstakingly erected were gone, and Misato's bloodstained cross pendant lay around his neck. It was…shocking, to say the least, but still definitely encouraging. He smiled slightly, but his quiet peace was soon interrupted by a somewhat familiar voice.

"Hey, Shinji. You alright, bud?"

Shinji turned his head to his left, and saw Delta kneeling there, his face still alight with that ethereal green aura and clad still in the clothes he had donned in the course of his prior intrusion into the Third's psyche.

"I'm…fine. Thank you."

"Don't mention it, kid. Just doing what I needed to do," Delta said while helping Shinji up. As Shinji looked around, his vision strayed to Asuka and Rei, their prone and unconscious forms both causing him to wince as he recalled the earlier experiences concerning them. However, this soon fell to the sidelines of his thoughts as his gaze turned upon a rather unpleasant sight. It was Omega, no longer clad in the forms he had used for the abrasive forays into the unconscious minds of the three Children. Shinji also saw Omicron, but he was looking towards the sun, his manner eased and calm. However, Omega seemed…sullen? As he approached Shinji, the teenager stood his ground, prepared to fight this time, if necessary. However, the words he heard next weren't at all to the order of his expectations…

"Walk with me, Ikari."

Shinji swiftly acquiesced, glad to have averted a confrontation with the being that had nearly broken his mind. He quickly joined Omega on a walk across the beach, listening to the waves' rise and fall as the tide ever so slowly ebbed. After several minutes of only hearing the waves, Shinji decided to break the silence; his thoughts had kept returning to their previous encounter, or to other recent events, and he desperately needed a break. "Err…what did you want to talk about?"

"…I cannot put into words the remorse I feel over my actions. What was initiated as my desire to restore the Lilim had nearly ignited an even worse disaster. However, thanks to those unseen by Lilim for three centuries, things will be slowly set right."

"What do you mean?"

"The Lilim population will return to its previous state before Third Impact over the course of five years. Those who perished before and during Third Impact will be able to return to their physical forms, as well. The Earth's axis is also slowly changing back to a state before fifteen years ago, when the event known as Second Impact occurred."

"Why so slowly?"

"We need to preserve our secrecy, for now. Nobody except you knows about us, and until a day described to us by leaders past, we will leave the Lilim alone. Those Nightfire and Nufire that migrated to Earth will remain here to observe the progress of your rebuilding."

"Will Delta be staying here?"

"Yes, actually. You two seem to have built a bond that I have never seen before…and that bond has given me hope for the future. If a Nightfire apprenticed to me, and a Lilim with your past could bond together, perhaps the Lilim and First Ancestral Race could meet face-to-face sooner than we expected."

"…And why did you want to poison Ayanami and I against each other?"

"She is incapable of bearing children, because of the Super Solenoid Organ in her abdomen. If you were to have chosen as things were, when you two died, the Lilim would have been finished. However, I have realized that forcing two people together is…morally incorrect."

"Children? But then…" his face paled with the realization of what this implied.

"Yes, we sought to recreate the legend known as the 'Garden of Eden'. However, it appears that your choice is Lilith rather than Eve."

"So, what will you and Omicron do now, since your task is completed?" The subject was change quickly as conflicting feelings filed into Shinji's mind, ones, which he would prefer to think about later.

A few seconds later, a gigantic shadow overtook the beach. Not only did it envelop the beach, but also almost the entire area. The scope was such that Shinji was unable to discern where it began to where it ended. Glancing skyward, he beheld something truly amazing, even to a person of his rather extended experience. His eyes boggled at the sight, and he stuttered trying to make words.

Floating above him was a space vessel of tremendous size, though still appearing sleek and maneuverable in form. It was cylindrically shaped, almost like a pen in form. To the stern, an impressive engine array, and the bow of the vessel were lined with various sizes of communication antennas. The bridge was located near the engine array on a horizontal spine extending outward, but it seemed small for a vessel of its size.

Finally, after several moments of stuttering, Shinji managed to string the errant syllables that had been emerging into words,

"W-what…is…that?"

"This, Ikari, is my vessel. Her name is Tycho Longinus; named after one of the craters on your satellite, Luna, and the weapon you refer to as the Lance of Longinus, deployed with all the Seeds of Life as they were spread across the universe. As you can see, she is very large. However, my species makes use of various numbers and numerous classes of large vessels like these. This was formerly a standard Heresiarch-class heavy battleship, but I chose her as my personal vessel, and modified her accordingly."

"You came here…in this?"

"Yes. This is our home away from home, and it serves the purpose quite well. I believe it is time to say goodbye…" Omega said as he waved his right hand, and suddenly, the pair was back where Omicron, Delta, Asuka and Rei were.

"Delta, I'm leaving Earth in your hands. Send me monthly reports on the progress of Reconstruction."

"Yes, Master. It will be done," Delta said as he bowed for his Master and friend. Omega extended his hand towards Shinji, hoping for a handshake. Shinji, feeling a little forgiving, decided to shake it.

"Perhaps you can forgive me in a few years?"

"…Maybe."

"I understand. However, I offer you one piece of advice, in the spirit of reconciliation; do not allow your fears to dominate you. And now, this is our farewell, Ikari. Meeting you has certainly been…insightful."

Omega backed away from Shinji, and Omicron walked forward, grabbing Shinji in a headlock and giving him a playful noogie. After the noogie was finished, Omicron said to Shinji, telepathically, "Good luck, kiddo. Thanks for helping my bro. I don't think he'll be so stuck up anymore."

With a slight struggle against the close contact, the boy managed to reply,

"Um. T-thanks. It was n-nice meeting you…"

After their short goodbye, Omicron joined his brother, and they raised their heads towards the underbelly of Tycho Longinus. Suddenly, a super-bright violet light began to materialize around them. Their bodies began to disintegrate, or so it seemed. As their forms slowly vanished, Shinji could only watch in amazement as they returned to their 'home away from home'. Finally, after a few seconds, the brothers were aboard their ship. Shinji watched as a beautiful, ethereal light began to form around the colossal vessel, and just in a few seconds, the ship disappeared into subspace.

Shinji then turned to where Delta was, but he was no longer there.

Unbeknownst to Shinji, while he was watching Omicron and Omega return to Tycho Longinus, Delta had decided that now was the best time and focused his energies into his hands. Once he had managed this, he opened a portal into his domain and quickly stepped through. It was from here Delta lived, and it was here that he would stay…he wasn't particularly fond of good-byes.

Now, all Shinji could do was wait for Asuka and Rei to get up and come up with some cover story that would somehow explain all that had happened in the past seven days. But, before that, there was something he had to think about. Sitting upon the sand near their unconscious forms, he reflected on the words of the other. If Eve were Asuka, then that would have made Rei 'Lilith'. Omega had said he'd chosen her. Was that true? But wasn't he afraid of her…?

But, looking upon the unconscious girl, memories came back; this was the girl who had smiled for him after almost dying to protect him. The girl who had died to save him. How could he be afraid of her? But then, said another part of his mind, she did die. Is this the same girl who did those things? And the fear threatened to return, but the fear was beaten by Rei herself.

With a quiet groan, crimson eyes inched open, and for a moment their gazes met. Shinji's emotions suddenly flew into a whirlwind, whilst Rei's mind processed the image of him in the same instant that it became consciously aware of the memories from her former self. Without conscious thought, a small smile came to her lips; that which she had only used once before, for the same audience.

'Ikari…'

However, she was unable to look up at him for long, because Sol's light quickly forced her to blink. But it didn't seem to phase the other pilot, who in much fear had just melted at the sight of the smile. And hadn't Omega said he shouldn't let his fears rule him? Offering her a hand, he said quietly,

"Welcome back, Ayanami."

Accepting his offer, she was able to rise, and began to inspect the area after replying with an equally quiet, "Thank you." While not the first time she had used words of gratitude, doing so still brought a very slight flush to her cheeks. Moreover, though, it crystallized something for Shinji.

A mad blush threatened to overtake him, he failed to release her hand, drawing her attention back to him as he managed to string some very difficult syllables together, "A-Ayanami…I…I think I h-have feelings for you."

As soon as it was done, he tried to break away, fear of rejection having already taken over his mind, but this time it was the blue-haired girl whose grip wasn't released. Looking back with the slightest bit of hope taking root, he was quite surprised to hear, "Ikari…my life was given up freely for you. How is it that you could doubt that your feelings are reciprocated?"

And then, without much thought, their lips met. It was neither a long kiss nor an especially passionate one, and neither expected it to be. But it was…nice.

Well, that's it. Everything turned out all right in the end, but this time, it was pulled off in true Evangelion fashion. I was actually planning on a sequel, but after a heated discussion with CyberForte, we agreed that this is where it will end. We'll leave you to guess what happens next. So, thanks for reading this and reviewing. Good night, and good luck.