A/N: This is my thoughts/version of Yui Ikari's connection to SEELE, et al, as pertains to this universe. Some things will be different, of course. But, I think it works for the story.

CH. 45: FLASHBACK - THE IKARI CONNECTION

-In the year 1998…

"I understand congratulations are in order, General," a spectacled man in a brown business suit said as he spoke on a satellite phone with one of his 'agents' currently deployed in Bosnia. "You've certainly earned the promotion."

"Thank you, sir," the man on the other end of the phone said. "And I do have good news for you. The relic has been confirmed as authentic. It was located right where your people said it would be."

"Excellent," he replied. "And it's been properly secured?"

"Your 'recovery team' was able to extract it from the site and depart the country without drawing attention. They're almost as good as my old Delta team."

"ShadowCO employs only the best. Perhaps someday in the future they can be of further assistance to you."

"I wouldn't mind it." The General replied casually. "But, I couldn't help at marvel at the measure you took to retrieve something that most consider a myth or a hoax.

"It's a personal matter. It once belonged to my family. I've searched long for this relic ever since it was…misplaced back in the 1940's."

"Well, estimates are that the bunker it was hidden in was constructed by Tito himself in the summer of 1942 and then abandoned and sealed in the winter of 1943 or early 1944. That coincides with the Nazi's retreat from the region."

"I'm aware of the region's history, General," he replied. He finished hitting some keys on his computer, making adjustments for wiring money. "In the meantime, I've already forwarded your fee to your account. Do not worry, it'll pass any inspection by any tax auditor."

"As they say it's been a pleasure doing business with you, Mr. Crowley."

"Same for you, Brigadier General Shepard," and with that Crowley hung up the phone. "Over fifty years…" He muttered to himself. 'I never should have lent the Spear to that fool Adolf. To think he believed its presence would guarantee his victory. I had suspicions of its true worth but I let that oaf talk me into…' He took a deep breath to calm himself. 'Doesn't matter now. By morning it will be locked back in a vault until it is ready to be used.'

"You should've let me handle the recovery personally," the man sitting across Crowley's desk spoke up. "We never would've had to risk so much by outsourcing such an important operation."

"We've been over this, Cortez," Crowley replied. "We've handled issues directly in the past but as we learned so painfully, our direct involvement raises too many questions. We tried it with direct control over the East India Company and we were nearly rooted out."

"I know," Cortez groaned as he adjusted his bow-tie. "I'm not saying we return to the EIC model entirely. Just for certain sensitive matters…"

"I understand your concerns. I also would like nothing more than to personally see things done. But, our methods have kept us secluded for centuries and it is our ability to operate from the shadows that is our greatest strength."

"Still, we must be careful which 'agents' we chose to employ."

"The choice we made to back that simple-minded failure of an art student was a rare mistake," Crowley conceded. "Nothing is ever without a few flaws."

"I just wish I was the one to put the bullet in his brain…"

"I would've preferred killing him in one of his own camps. Monstrosities and a waste of resources…"

"I'd best be going," Cortez got up from the chair. "That Afghanistan situation isn't going to resolve itself. The Northern Alliance is moving slowly and I fear the regime is getting too close to certain individuals."

"Understood. One quick question before you go," Cortez paused to listen. "How's the Y2K farce coming along?" Cortez chuckled a good bit.

"It's doing its job of tying up certain resources. Some politicians even think it'll cause their nuclear missiles to spontaneously launch."

"It never ceases to amaze me how stupid some of the so called 'people in power' can be." Cortez tipped his head and exited the office.

And with that Crowley opened his email and saw another update from his rising star. Her studies in Japan were going well and she's begun seeking out professors under whom she could advance her education. Crowley had a few suggestions but he would trust her judgement. Yui Ikari had a knack for finding the right teachers.

XXXXX

"Hmm, let's see here," Kazou said as he looked through Miss Ikari's file. He had read her thesis paper on 'Mechanical-Biological Engineering and Human Evolution'. It made for an interesting read. It even intrigued him, even though it was largely theoretical and a different subject than his focus, which was Theoretical Physics.But, she came recommended by one of his colleagues at the university. And apparently, she was seeking him out to study under.

Normally, Kazou Fuyutsuki wasn't an arrogant man. He liked to think of himself as a humble professor whose mission in life was to educate the young. But, he couldn't help but feel a swell of pride whenever a student specifically requested him to be their teacher. And when said student comes recommended from another faculty member it usually meant the student had promise.

"She graduated with a Masters in Biology from Tokyo at the age of sixteen? Impressive. What else?" He moved on to her other schools. "Distance learning courses in Computer Science from MIT and Mechanical Engineering from Purdue in the United States at the same time? Wow." Looked like Yui Ikari was a progeny and not content with mastering only one area of expertise. "A true Renaissance Woman of Science." He decided the rest of the file to wait, since he saw her arrive in his office.

XXXXX

"Miss Ikari has begun her studies in Kyoto, Mr. Crowley," Samantha Steward, a fellow committee member of MAJESTIC, informed him. "He may be Japan's leading scientist on the matter, but I have doubts about him."

"What specifically do you have issue with?" Crowley asked her as he read a report from one of his science teams.

"He seems to be highly outspoken on the ethics of applying evolutionary sciences."

"The ethics of man can be manipulated," Crowley replied. "Case in point, Hideki Ikari."

"Her grandfather?"

"Yes," he grinned. "Interned at Manzanar at the beginning of World War Two he still decided to enlist in the US Army. His knowledge in structural engineering became useful during the war and he was deployed as a demolitions specialist. Served with distinction, as I understand." Crowley's computer beeped informing him it had finished deleting some old files and that the hard drive had been reset to factory condition. One had to be careful not to leave a trace. He'd learned that long ago.

"You're saying his knowledge of how to build radio towers was 'twisted', in other words, into practical knowledge on how to blow up enemy bridges?"

"Exactly," Crowley smirked as he leaned back in his chair. "The knowledge of construction used to practice destruction." He set the report down and walked to his office door. "One just needs to find the right motivator."

"Don't you worry you're putting too much faith in Yui?" Steward asked. "She may be your de facto-"

"Her almost unique affinity to science, not to mention her eidetic memory, will advance our timetable by generations," Crowley cut her off. "Otherwise we'd need to recruit at least a half-dozen scientists, if not more, to match what she alone could accomplish for us."

"And the fact that her father was your lieutenant…?"

"A stroke of fate. As was his…unfortunate death…"

"Yes," Steward smirked. "The hit and run…A real tragedy."

"Don't be coy," Crowley cautioned her. "It's beneath us. Remember what I told you so long ago, Elizabeth?"

"Don't remind me," she growled. "And don't call me that. That's not my name anymore."

"Doesn't matter," Crowley countered as he stopped to look outside. He always had a fascination for this country's architecture. "What matters is how are the plans for SEELE coming along?"

"On schedule," she reported as shifted her shoulder bag to the opposite side. Through the windows in the hall they could see the city of Bern, Switzerland. She'd never admit it but she was somewhat jealous that Crowley spent so much time on Yui Ikari. Almost like she was his own daughter. But Crowley had never fathered any children. He still held on to that ancient vow of celibacy despite his heretical leaning.

"And the Katsuragi Expedition?"

"We still need to assign an 'advisor'," Steward reminded him. "Dr. Katsuragi is too low ranking in our science branch to be fully trusted with reaching the goals we set for the South Pole teams."

"And you're sure that what we seek is down there?"

"Have I ever been wrong?" The woman smirked once more.

XXXXX

Later that year, Crowley received word from his protégé concerning a promising recruit for MAJESTIK. "Gendo Rokobungi," Crowley read the name. "A bit of a maverick when it comes to authority but he's got three degrees in physics and engineering."

"Her report reads almost like a diary entry," Ian MacReady, another MAJESTIK committeeman said. "I wonder if her judgement is clouded on the matter."

"She sent reports on him before they began their 'elopement', as it were," Crowley responded. He thumbed through Rokobungi's public records. "I'm more troubled by his brushes with the law. Nothing serious and it would appear, he was not the instigator of these incidents."

"But having such a punk could invite scrutiny if he got into serious trouble," Steward added. "On the other hand, if he had a stabilizing factor, these incidents could conceivably end. Particularly if he were to be sent out of the country."

"You suggest sending him on the Katsuragi Expedition?" Crowley asked. "As what? A test of his loyalties?"

"In part, yes." She nodded and handed over the preliminary report from the satellite scans. "It would be a big risk to send someone more important to SEELE's mission…"

"SEELE hasn't been stood up yet," MacReady countered. "It's too soon. It's not ready…"

"Few things are as ready as we'd like," Crowley said. He gave it some thought. SEELE, the organizational shift that MAJESTIK was preparing for, was partially the work of Yui. Many of her ideas were pulled from MAJESTIK programs to be integrated into SEELE. "And the longer we stay on any one program the greater the risk of exposure."

"You still fear a repeat of the Salzburg Incident…" Steward rubbed her forehead. "We never had another breach of that caliber and the possibility-"

"Only because of the actions we took in the years after," Crowley replied. "One of which is our occasional organizational shifts. We considered one when the Iranian Embassy was taken over. Luckily, a contact we had in the SAS was able to ensure we weren't exposed. But, MAJESTIK has existed for nearly half a century. That's been long enough…" He took a deep breath and set Gendo Rokobungi's file down. "But we digress. I'll inform Doctor Ikari that we'll accept her recommendation on a probationary period. Rokobungi will be assigned to Katsuragi but he will have a short leash. Will that be acceptable?" Steward nodded. Even if she objected it would be pointless to argue with Crowley once he made up his mind. "And we'll begin the transfer to SEELE at the beginning of the fiscal year. Nothing must seem out of place, lest we invite scrutiny."

"And the new identities?" Steward asked next. "Will we be transitioning, too?"

"Might as well," MacReady suggested. "It would prevent suspicion if the managers of MAJESTIK appeared on the board with SEELE and then 'disappeared'."

"Agreed," Crowley nodded.

XXXXX

-In the year 2000…

The white of the snow and ice outside reminded Gendo of wedding dresses. Admittedly he never imagined himself to be the one for marriage, let alone to be the one who made the overture. But, Yui was indeed special. It sounded so corny; 'that special someone', but it turned out to be true. But her warm nature and her willingness, and even devotion, to look past his faults touched something within him. And it was her word that got him this assignment in the first place. He would not prove her faith in him misplaced. He'd prove himself to her and her benefactors.

His attention was drawn back to the computer when he heard the gong sound effect alerted him that the files had been copied. He ejected the CD and placed it in his briefcase along with the other copies, both in soft and hard copy form, from the expedition's research into the 'ADAM' and locked it. He double checked the weather report, lest his flight tomorrow be canceled.

He didn't understand why he had to leave before the experiment. He also didn't understand why Crowley recommend he deliver the materials in the briefcase before his wedding to Yui ahead of their originally planned date. But, again, he would prove himself. The weather looked perfect for flying back to McMurdo. And the C-130's could fly in almost anything Antarctica could throw at them. He'd be back to his fiancée in two, three days at the most. He smiled at the thought.

-One week later…

Their retreat was far off to the north of Sapporo. And the worst areas affected by the 'tremor' that occurred at the south pole were the south facing coastal regions. That and the weather shifts had already begun to be noticed in Europe and North America. NASA and the Russian Space Agency were already estimating that Earth's alignment had shifted at least 10 degrees. The full extent of what that meant was still being debated.

Compounding the matter was confusion over what had caused the tremor and shift. At least, there was confusion amongst governmental and private entities. There wasn't much confusion at a non-descript office building in Switzerland. There, a handful of individuals sat in silent contentment and reflection on what they were already calling 'Second Impact'.

The result of Katsuragi's 'Synchronization Experiment' was not what was intended, but, the information Gendo Ikari, formerly Rokobungi, had brought back had enabled SEELE to hypothesize corrections to their scenario. It also helped shed new light on certain segments of the Dead Sea Scrolls. They were also going over the formulation of a new puppet organization to oversee the Instrumentality Project, tentatively named GEHIRN. Already they were unanimous in their selection for its directors: the newlyweds currently riding out the devastation in Northern Japan.

XXXXX

-06 June, 2001…

He had her eyes, Yui could already tell. She could also tell that he was going to be strong one day. His lungs were strong as was his appetite. Despite still being partially covered in birthing fluid, Shinji was the most beautiful thing she had ever seen. And, for this new mother, it was love at first sight.

Across the world, there was some concern among parents that bringing a child into this world, the post-Second Impact world, was almost criminal. That things looked so bleak that to force a new human being to live through it was wrong. Yui was not one of those people. Quite the opposite; seeing Shinji taking his first breaths of life convinced her that the future was bright. Brighter than anything she could imagine.

"Anywhere can be like Heaven," she said to her husband as he thought about how difficult it would be to raise Shinji in 'Hell'. "He has a chance to be happy anytime, because he's alive." It was a familiar theme with Yui. A theme that never ceased to make Gendo believe in her vision.

Her belief that human will, and humanity,was stronger than anything that could happen to them. Humanity was a race of survivors; plague, famine, wars of genocide, ice ages, every human being on Earth has ancestors that faced down and survived them all. And now, newborns had ancestors that survived a potential extinction level event.

"I see," Gendo nodded as he held Yui's hand. "You're right."

-In the year 2003…

Yui Ikari, the Interim-Director of GEHIRN, was conflicted. On the one hand she was the image of dedication. It's what allowed her to study three different majors at one time years ahead of most college students and obtained both her PhD's before her twenty-fifth birthday. A week ago she was dedicated to getting GEHIRN off the ground and Project-E on schedule.

But, then, she overheard an argument between her former Professor and her husband. An argument over Second Impact. She then did a little digging into SEELE's records and saw the same things Fuyutsuki saw. But, what she inferred from her analysis was worse than what the older man realized. SEELE's hands had the blood of nearly three billion people on its hands. Even if they didn't intend it, the results were the same. And the fact that they covered it up only made it worse.

With this in hand, she began to look at GEHIRN and Project-E with new eyes. Before she had the eyes of a scientist. Now, they were the eyes of a mother. And a mother's first instinct is the well-being of her child.

"I'm bothered by the use of LCL for the control system," Yui said to her husband as they sat down to dinner. Yui set some mandarin oranges in front of a happy Shinji, thus far his favorite food. "You do know what it really is?"

"It performs better than any synthetic mixture or artificial connection developed thus far," Gendo replied. "I admit, the idea of using it is disturbing. But what other choice do we have? Dr. Akagi's theories on an artificial guidance system are still a work in progress."

"Mommy?" Shinji asked. "What is art-a-face-shoal?"

"It means fake or not real," she smiled at him. "You know your stuffed animals?" He nodded. "They're not real animals. They're artificial."

"Oh, okay!" Shinji smiled. "Like daddy's new tooth?" Gendo coughed and tried to excuse himself from the table.

"His…tooth?" Yui quirked an eyebrow.

"Yeah, he said he had to go to a doctor for a new tooth!" Shinji exclaimed. "I heard say it on the phone. And he's too old to lose baby teeth." Once again, Yui couldn't help but be amazed at how smart Shinji was for an almost three-year old. He was still working on his pronunciations but his sentence structure was that of a kindergartener or even first grader.

"Gendo, dear?" Yui asked in a sweet voice. "I thought you said the cavity was under control?"

"It is," Gendo replied. "In that it's no longer there." Yui just sighed before picking Shinji up and taking him to bed.

As she was tucking him in Yui began to think on the new method for construction being used on the new Evangelion. The Mark.01 prototype model, hadn't even been finished yet but GEHIRN was already building the Mark.02 test platform. And there were already plans being drawn up for a production and advanced production models. Throw in the concept designs for Mark.05 and Mark.06 and Yui couldn't help but think there was something else going on. SEELE was moving the project too fast.

"Goodnight, sweetie," she cooed as she kissed Shinji on the forehead. "Have sweet dreams and always remember: mommy loves you." And with that she stood up, turned out the light and slid the door shut.

Shinji. Her baby boy, and the true love of her life. Before she had him, she thought that the work she was doing at GEHIRN and for SEELE was a good thing. That the end result would make things better for him. But, now…when she thought about the Instrumentality Project and the 'prison' that had just been built for Lillith…the dots were connecting in a way she did not like. Especially what it meant for Shinji.

Watching him learn to walk, learn to speak and even how he was able to quickly figure things out never ceased to impress her. Just after he turned two, Shinji was not only raiding the snack jar but also finding it no matter where she hid it or how well she secured it. He always seemed to find a way to get to it. His problem-solving skills were almost scary!

And it was because of his uniqueness that she began to question the theories behind Instrumentality. The idea of ridding the world of 'chaotic forces of anarchy' seemed noble. But, as she thought on it, on a more philosophical level, she realized that one could not do away with such forces without also doing away with free will; with individuality.

And that, is what caused Yui Ikari, the chairman's favorite star, to have a change of heart. How could her son be amazing as he is now if he was not allowed to be unique in his own way? To choose his own path and make his own future? The answer is simple: he couldn't. And Yui couldn't allow that.

Gendo was hard headed and couldn't understand all that. He still felt that one could control things without losing free will. And his determination to show up the chairman was another source of aggravation. Tonight was one of the rare nights he was home, he was always working on Project-E and trying to show 'Keel' that he was more than capable of running the show. Yui tried to tell him that he was trying too hard, but he still kept working.

It made things difficult for her. But, not impossible. She had a plan to throw a wrench in SEELE's plans, one that would go unnoticed until it was too late. She knew how to pull it off and she'd be there for Shinji to see it happen. She'd be able to watch him grow up, go on dates, and have a family. And she'd be there for all of it. In the meantime, SEELE would go forth with their plan not knowing that the foundation for their downfall had already been sown: by a mother scorned.

She had it all figured out. After all, she was a genius.

But, she forgot one thing: the Evangelions were still new territory…

XXXXX

-2004

"Whose child is this?" Fuyutsuki asked as the boy smiled up at Naoko and waved. She gave a soft smile back and turned away from him. The boy then ran to the glass window to look into the test bay.

"That's Ikari's son," Naoko replied. Although he detected a hint of jealousy in her voice, Fuyutsuki let it go.

"This isn't a daycare center," the old professor grumbled.

"I'm sorry, Professor," Yui laughed over the radio. She was down in the test chamber where the still incomplete Mark.02 Evangelion sat reclining in a pool of LCL. Its legs were still bones and the synthetic flesh was still being grown on them in the LCL. However, the central control systems, it's nerves, as it were, were fully functional. "I'm the one who brought Shinji here."

"But, Yui," Kazou said in an almost fatherly tone as Shinji waved at his mother, "this is your experiment today."

Yui waved back at her little boy. She was wearing an experimental test suit that she had helped design. It was blue with white shoulders and had a locking collar for the helmet which she held in her hands. While the prototype was designed for a piloted cockpit, Yui had designed a 'direct connection' system that would make manual controls needlessly redundant.

The helmet contained the devices that would amplify the pilot's brain waves and convert them into a signal that the Evangelion would receive in the form of commands. In short, it used a primitive psychic-harmonics control system. And today would be the day she'd test it live for the first time.

What the others didn't know was that Yui had designed the system to not only receive commands but also 'dormant programming'. This programming 'error' would be completely untraceable and impossible to delete or remove. And yet, when the time came for SEELE to enact the final stage of their plan, whatever it would be, this Evangelion would 'revolt'. It would affect only this unit, a unit that SEELE held crucial to their plans. The single point of failure, and it would be Yui who would see it done. Today.

"That's why I brought him," she explained as she donned the helmet. "I wanted to show him how bright the future would be." And with that, she climbed into the entry plug. Little did she or anyone else know that she would not emerge.

"Starting LCL ionization," a technician reported. "Everything looks green across the board. Beginning to phase two."

"Engaging synapse connections," another technician reported. "Nothing out of the ordinary. In theory, at least…"

"Very well," Naoko Akagi agreed. "Initialize the Direct Interface."

"Beginning checklist," technician one confirmed. "Steps ten through fifteen cleared. Ready to engage the system."

"Engage," the woman ordered. The technician turned a key knob and almost instantly the facility turned pitch black and the control consoles shut down. Amber emergency lighting came on. "What happened?"

"I don't know," technician number two reported from her console. "As soon as the system engaged I saw a power spike and then everything crashed."

"Check the generators," Fuyutsuki ordered, not noticing the movement on the other side of the glass. "Make sure we didn't blow anoth-"

CRASH!

Something large and heavy slammed into the glass barrier and shook the facility, throwing everyone to the ground. "What's going on!?" Gendo shouted as more lighting came on in the test chamber. What they revealed sent chills down everyone's spines. "Oh no…Yui!"

The incomplete Evangelion was tearing at its own flesh and flailing about like a deranged man. It even began frothing at the mouth like a rabid animal. And the sound it made…a most terrifying combination of a growl and pained scream.

"Abort the experiment!" Gendo ordered. "Shut all power to this sector!"

"All our equipment is down, sir!" The first technician replied as the Evangelion crashed into the windows again. Shinji scrambled in terror underneath a desk. Fuyutsuki, raced to his side, putting his body between the boy and the rampaging monster in front of them.

"Blow all the connections manually!" Gendo ordered as Naoko and other technicians scrambled for cover. "I don't care if you have to cut with a fucking axe! Just cut the goddamn power!"

The windows broke away along with large segments of the control rooms. Multiple people fell down and either drowned in the LCL or died from falling onto concrete platforms many stories below them. When the power was finally cut, the facility went pitch black yet again. There was a final crash when the Evangelion collided with the observation platform, crushing even more workers.

When temporary lighting was restored and rescue began, over a dozen GEHIRN employees had been killed. But, one was still unaccounted for: Yui Ikari…

XXXXX

Not long afterwards the SEELE Council met to discuss the event. "Yui Ikari is lost to us," Larson, the man formerly known as MacReady, stated. "But all her research and her theories remain. We've suffered a loss yes…"
"She was our most promising candidate to lead GEHIRN once we brought it into public light for its ultimate mission," Holbrook, formerly Elizabeth Steward, interjected. "She was a natural leader. If she spoke, people listened. When she took charge and gave directions, people followed."

"So, who shall we place in her stead?" Blackwood, another member, asked. "Naoko Akagi has a similar level of intelligence…"

"But she does not possess the leadership abilities we need," Larson responded. "At the moment GEHIRN is still a scientific enterprise, yes. But eventually it will be undertaking a more militant role when the harbingers arrive. We'll need someone who can lead through such a situation."

"What about her husband? Gendo Ikari?" Blackwood asked next. "He knows about her work and her theories, as much as Dr. Akagi and Professor Fuyutsuki…"

"He's a bull," Keel retorted. "He's also extremely vain and not much of a team player."

"He's also got a strong personality," Holbrook countered. "He may not be the inspirational figure that Yui was, but he's able to get people to act."

"I agree," Larson nodded. "Trying to find another candidate would take too long and there is still much we have to do before the others wake up."

"Not to mention he's was Second in Command at the time of the incident," Holbrook added as she adjusted her glasses. "It's the natural choice."

"And let's not forget," Blackwood continued on. "He took charge in the chaos following the incident with the test model. GEHIRN personnel, including Akagi and Fuyutsuki followed his lead. Whether it was because he was already in the position or because his direct manner got them to act doesn't matter. What matters is he got them to act."

"Very well," Keel grumbled. "We'll leave Gendo Ikari in place as the head of GEHIRN. If he proves capable of providing results we will keep him in place."

"We will also need to find a means to stunt Lillith's growth," Holbrook changed the subject. "Katsuragi had the Spear with him when…"

"We have reason to believe that the Spear has achieved its transformation into the key we need to unlock Instrumentality," Larson replied. "The only problem is that it's located under nearly a mile of water."

"We can't mount an expedition to recover it just yet," Holbrook grumbled. "It'll raise too many suspicions."

"We have other methods for preventing Lillith from regaining full strength," Blackwood spoke up and he shifted his glasses. "They're messy and costly but they'll suffice until we can recover the Spear."

"Do it," Keel ordered. "And make sure that as soon as practical…"

"It'll take a few more years," Blackwood reassured their leader. "But it'll be recovered."

"I just hope the Angels don't arrive before then," Holbrook countered.

"What do you think the Evangelions are for?" Keel smirked in reply.

Yui Ikari was listed as having died that day. Shinji, her son, was almost immediately sent away by his father. The boy kept asking "Where's mommy?" and "Why can't I stay, daddy?" He got no answers. And it would be a pain that would not go away. Losing one's mother is the kind of pain that never ends. Same with being willfully abandoned by a parent. The damage such things do to one self is never easy to heal.

Yui Ikari never meant to leave her child alone in the world. Nor did she intend to have him be so traumatized by her 'death'. But, her mission to thwart SEELE's goals was not over. And her son was destined to play a role.

And for Shinji Ikari, he would soon learn other kinds of pain. And he would learn new ways to deal with them…