Disclaimer: See prologue
Chapter 2: Birth and Death

Hakone, Japan, 2007

"Each and every living thing in this universe contains the manifestation of the soul, and it is this facet of living beings that gives organisms of massive stature their ability to generate a physical projection of that soul. The research done on the Third Angel at Bethany Gehirn proves that the AT Field is not some field of plasma or electricity, but an extension of the soul created by a being with the sheer force of will to force their individuality onto the world around them. Even creatures like whales and elephants here on earth are capable of creating an AT Field; they simply lack the cognition to perform the action necessary to generate the field."

SEELE-03 SOUND ONLY—"And as such, these adversaries are not just thoughtless animals, they clearly have a set goal and purpose for their invasion."

SEELE-01 SOUND ONLY—"And the Scrolls have stated their purpose: When they unite with the progenitors of life in this world, Adam or Lillith, the mortal inhabitants will be eradicated in place to create a new race, one that possesses the Fruit of Life over the Fruit of Knowledge. In that account, the Second Impact failed, as the Third Angel did not complete its unity, and the remains of Adam were fossilized in the Antarctic ice."

"Indeed, however, it is the Fruit of Knowledge that gives us the power to fight these beings, and I assure you, they will not unite with Lillith."

SEELE-01 SOUND ONLY—"Remember Ikari, the 'Third Impact' is not what we are fighting, it is the Angels' control of it that we will not allow. The Impact itself is our key to the Forced Evolution of humanity into eternity, and it will happen under our hands."

SEELE UNITS (Various)—"INSTRUMENTALITY! INSTRUMENTALITY! INSTRUMENTALITY! INSTRUMENTALITY!"

"As long as Gehirn possesses Lillith, gentlemen, I assure you, Instrumentality is your possession."

The room darkened as the holodeck ended the conference with the shadow government leaders.

"They still don't trust you, Gendo," Fuyutsuki stated.

"And it does them good. You know I have no desire to 'Evolve Humanity'. Instrumentality is merely what will bring Yui back to me."

Gendo picked up his office phone and dialed Dr. Akagi's extension. "What's the status on the extraction, Naoko?"

"In theory, we should already be done. The MAGI have confirmed that electrified LCL can be used to transfer a human persona from one physical body to another. They also determined that Yui's soul has, at a minimum, survived and is still residing inside Unit 1. We've made several attempts to draw her out."

"But you haven't…"

"I don't know how to explain it, sir, but Unit 01 is actively resisting the extraction attempts. Either Unit 01 doesn't want her to leave, or Yui herself is refusing to cooperate with us."

"Then I expect you to make continued attempts to get her out. What's the status on her new body?"

"Yui's DNA donations weren't enough to recreate her body alone. We found our solution in several skin grafts taken from Lillith's body. With Lillith's dominant DNA ,we were able to create several replicas, and are currently holding the most cohesive body as Yui's future vessel."

"Then I have two orders for you: restart the cloning process from scratch. Build Yui a body with everything you've learned so far. I want it to be perfect."

"And the other, Gendo?"

"I will be referred to as 'Commander' and nothing less. Can you understand that?"

"…Yes, sir."

"You will perform an LCL extraction from the comatose body of Lillith into your best current clone."

"You want me to do what?"

"It will be another layer of protection against an Impact. If an angel reaches Lillith, it will find a dead body."

"Lillith wouldn't be dead, only dormant."

"Even so, we still need the protection."

"Very well, sir."

Edo, Japan, 2010

Nine-year old Shinji Ikari deeply loved his long-lost mother, Yui, but to this day he still became depressed whenever thoughts of his father would enter his head. To Shinji, instead of 'Gendo Ikari, my dad' he was 'Gendo Ikari, the man who let those government men take me away'. Shinji wasn't in a bad position, however, as his legal guardian, who Shinji simply referred to as 'Sensei', was his wise and kindly fourth-grade schoolteacher. He understood Shinji's loss as he himself suffered through the death of his wife before he took Shinji in, and though he was stern and strict, raised him with grandfatherly guidance at every turn. Sensei didn't just dismiss Shinji's disdain for his father, but told him that his father's work was dangerous and life-threatening and that "What he does will help protect the entire world". It was Gendo's act of sending him away was the only way for Shinji to get an education and a childhood, Sensei told him, but despite his best efforts, Shinji never really believed him.

"Shinji, you're going to enter Junior High next year, and I want you to study hard and get strong and fit as well. You could try out for baseball or soccer, and you'll start taking lessons in defense-"

"Sensei", Shinji cut in, "I can play a sport, sure, but I don't want to fight anybody."

"Indeed you don't, and that's one of the many ways that I can see how well-behaved of a boy you've become, but schoolyard bullies, especially in your high-school years, want to fight simply because they can. You have to learn the difference between a threat that you can flee from and escape versus a threat that you must face and overcome. Your desire for nonviolence could be met by those who would do you harm, and I won't allow myself to let you go unprepared."

Shinji thought for a moment, "Is there anything I can do that doesn't involve me attacking people?"

"Indeed there is, Aikido is a wrestling form that teaches you to outmaneuver and overpower your opponent without brutishly beating on them. If a bully starts rushing towards you to hit you, you simply catch him and throw him to the ground, you don't have to hit him back."

"Ok, I'll try that, and I'll go for baseball when spring practices start."

"Very good, Shinji. I don't want you to become a high-school jock, I want you to become a strong and understanding individual, and that means you have to exercise your muscles and your intellect in equal measure."

"I will, Sensei."

Gehirn Headquarters, 2010

A cheerful four-year-old girl scampered throughout the massive pyramid complex, looking for the nice lady doctor the Commander told her to find. She split her time between taking school lessons with the Commander and his friendly old assistant—she was miraculously intelligent, already reading high-school level novels at her age—and getting regular checkups with Dr. Akagi. She didn't really like that last part, because it meant getting poked with cold metal things and having her head scanned by a big, noisy machine. But today the Commander just told her to find Dr. Akagi and tell her a secret.

She found the doctor typing away on a computer deep down in the sublevels; after watching her work without pause for a good few minutes, little Rei made a soft cough, awakening the scientist from her work.

"…Rei, what in the world are you doing all the way down here?"

"The Commander sent me to find you and tell you!" She happily answered.

"Okay then, tell me—you've got my undivided attention."

"The Commander wanted me to tell you that I think you're an old hag."

Dr. Akagi's face fell, "Rei, why would you say that?"

"The Commander wanted you to know. He calls you 'that old hag' all the time. 'The old hag is here' 'The old hag left' 'The old hag needs to go'…"

As Naoko reacted with shock, formerly happy memories flooded into her head. = "Commander, the Lillith transfer was successful, but we didn't create a human goddess. Instead, you've essentially brought a baby girl into the world."

"Yui always wanted a daughter after we had Shinji. We would have named her 'Rei'. I'll raise her as my own daughter, for the sake of Yui's legacy, Naoko." =

Naoko had been betrayed. Commander Ikari had just used this innocent little girl to break the doctor's heart. Naoko snapped.

By the time she had regained control of her emotions, Naoko saw Rei's lifeless body held in her own hands. = I just murdered a little girl = she thought, as she saw the sparkle of life in Rei's deep red eyes die away. She looked at Rei's beautiful natural blue hair, and saw the death of the most unique, individual child to have ever walked the planet. Naoko fought back the urge to vomit as her vision went blurry; she stumbled backwards…and over the safety railing down into the MAGI infrastructure complex. Her body collided with the ground at the exact moment that Commander Ikari made another phone call.

"This message is to congratulate the newly-credentialed Dr. Ritsuko Akagi. We at the newly-reorganized NERV organization would like to offer her the position of 'Chief Research Officer'. She may reply to this offer of employment at her own discretion."

After completing that call, he made a second one to the Artificial Evolution Laboratory.

"This is Ikari. Prepare a transfer and a new vessel for the First Child."

A/N: So, how's it feel to be on the beginning edge of the main Evangelion continuity? I am proud to promise more action and shipping bait in the next chapter. Now how about some reviews, people?