Cyber Shinji

Disclaimer: If I owned Evangelion then Shinji would not have been screwed over.

"Talking"

'Thoughts'

"Radio"


Chapter Two

After Shinji decided that he would pilot Dr. Akagi had taken him to get a quick rundown on the Eva operating system. But not before he made sure that Rei was taken by the medics to a safe and secure area.

And now he sat in Unit 01's Entry Plug, A10 clips in his hair, listening to the command crew as they prepped the Evangelion for launch.

"Inserting Entry Plug."

"Plug-in procedure completed."

"Initiating first level interface."

"Flooding Entry Plug."

When those words were said an amber liquid began filling up the Entry Plug. Shinji wasn't particularly worried about it as he had modified his lungs years ago to be able to filter liquids so he couldn't drown. That was back when he couldn't swim. As long as the substance wasn't acidic he would do fine. However his sensors informed him that this was the same substance with the blood-like composition that the Eva had resided in. But still he thought it was important to ask the good doctor what was going on since he hadn't been previously informed of this and as far as NERV knew he couldn't breathe underwater.

"Dr. Akagi, would you mind explaining what you are doing." He requested.

"Don't worry; this is LCL. When it saturates your lungs it will directly oxygenate your blood so you won't drown. It will also provide some cushioning and will help enhance your sync ratio." Explained the faux-blond doctor.

As the LCL rose past his head Shinji calmly inhaled the liquid, filling his mouth and lungs with it. "It tastes like blood." He idly commented.

"Tough it out. You're a boy aren't you?" Said Misato over the speakers. Shinji chose to ignore the woman in favor of beginning his own set of sequences.

His internal systems began an in-depth analysis of the LCL but all the information would be stored away for him to look over later. Right now he had more important things to do.

'Begin Assimilation Procedures.' Doing the same as he did with Rei, Shinji injected billions, bordering on a trillion of nanites from his body directly into the Entry Plug. From there a portion that was injected would remain in the Entry Plug while the rest would move on into Unit-01 itself. Considering the size and mass of the Eva Shinji was sending every spare nanite he had into it, and then some. He even sent a few dozen into the A10 nerve clips.

Meanwhile in Central Dogma. "Ma'am, we are getting some irregular readings from the Eva's nervous system." Lt. Shigeru Aoba informed Dr. Akagi.

"What? Let me see." The doctor said leaning over his council. But no sooner did she think of having the Magi run a quick diagnostic did the irregularities cease.

"Is it something that we should worry about Ritsuko?" Asked Misato.

"Probably not. Unit-01 is the test type so there are bound to be a few quirks in the system. But keep me informed if you see anything else."

Back with Shinji. 'Nanite injection sequence complete. Proceed with Level 3 assimilation.' Shinji's assimilation had been a high priority emergency Level 1 due to the circumstances. At Level 1 the nanites were to assimilate with their host as quickly and safely as possible. At the lower priority Level 3 the nanites would first travel through the host mapping anything and everything, making special note of any important organ/computer systems. As this happened the nanites would be relaying all of the gathered data back to Shinji who would be overseeing the process to make sure it happens as it should be. At the same time the nanites will begin using whatever spare materials they find to start reproducing. But until Shinji gives the OK they would not start any modifications.

At the moment it was too risky to start upgrading Unit 01. The last thing he needed right now was for the nanites to shut down some critical system for upgrade in the middle of the upcoming battle. But with the information Shinji was getting he would have a better understanding of how the Eva works.

And one particular bit of information almost made Shinji go bug eyed. The Evangelion Was Alive!

It wasn't a fully biological organism as there were various computer systems, sensors, and equipment built into the body such as the internal battery. But still the majority of it was biological in nature. It just wasn't like any biological organism that Shinji had in his data banks.

No, that wasn't entirely true. Some of the latest data told Shinji that Unit 01's DNA was surprisingly similar to one specific organism. The Angels. 'Oh Hell!'

It took all of Shinji's self control not to physically react at the information. As shocking as it was he would have to contemplate on how NERV created an Angel, even an incomplete one judging from the inactive genetic sequences, later. Right now he needed to deactivate all the injected nanites to prevent them from initiating one of their core programs.

In the event that the Enemy ever managed to inject one of their numbers with nanites to enhance themselves, not they ever showed particular interest in doing that, the nanites were programmed to attack the body from within. They would be literally breaking the Enemy down cell by cell. Again, in case the Enemy ever actually gained an interest in technology as a safety precaution the program was imprinted as a core program, where it was impossible to remove.

If Shinji wanted to use the nanites in conjunction with Unit 01 in any way shape or form he would have to rewrite the program. Something that would take weeks, if not months to accomplish. Assimilating the Evangelion with the nanites before that time would just be detrimental.

But there was one thing he could do first. Dr. Akagi had told him that he would pilot the Eva by synching with it thus controlling it with his mind instead of using conventional methods. Although they had still installed the butterfly handles to give something for the pilot to hold onto and use as a focus to help them move the Eva. It also provided a nice easy to reach place where they could put some buttons that were needed to operate systems that couldn't be controlled by synching.

The information the nanites had provided gave Shinji gave a basic idea of how the A10 nerve clips worked to enhance his synch ratio, and by using that concept with the nanites he could set up a more powerful system in the hairclip-like devices. It wouldn't be the most elegant or efficient system, but it should raise his synch ratio by at least a few points.

Back on the command bridge.

"The pilot has passed the absolute borderline. Bidirectional circuits are open." Said Lt. Maya Ibuki. "My God!" She exclaimed when she saw the numbers.

"What is it?" Asked Dr. Akagi looking over her assistants shoulders. "That can't be right."

"Rits?"

"According to this, Shinji's synch ratio is currently at 48.3 and rising." Ritsuko told her military counterpart. Typing in a few quick commands the results were verified. "Synchronization ratio is holding at 55.2 with a margin of error of 0.3 percent. Harmonics are normal. We can do this."

"Alright. Begin launch sequence!" Said Misato sending the Eva cage into a frenzy of activity to release the Eva from its restraints and to move it into position on the catapult. "Evangelion Unit-01 Launch!" Misato commanded.

Shinji could feel the G-forces shove him backwards into his seat as the catapult launched Unit-01 upward to the surface. And with only a slight jerk movement ceased, and Shinji was staring down the Angel through the eyes of the Eva.

"Are you ready Shinji?" Asked Misato.

"Ready and waiting."

"All right. Release final safety locks!" With that order the massive bolts in the Eva's shoulder pylons that kept it attached to the catapult sled were unlocked, freeing mankind's ultimate weapon.

"OK Shinji for now just focus on walking." Instructed Ritsuko.

The command crew waited with held breaths as they monitored Unit 01 and its pilot. They each leaned forward unconsciously as the Eva lifted its foot, moved it forward a little, and then heavily planted it back on the ground. The bridge erupted in cheers with Ritsuko crying "He's Walking! He's Walking!"

In the Entry Plug Shinji ignored the hollering NERV personal in favor of keeping his concentration. 'Easy there Shinji. It's not that difficult. It the same as controlling a digital avatar." In truth there were was a world of difference between controlling a body composed entirely of data in a world of data, and controlling a giant cybernetic alien that is the Eva in the real world. But the basic concept of using your mind to manipulate a body that is not your own was the same.

With that in mind Shinji took two more steps with confidence. Although he was slightly annoyed with the Eva's reaction time. By his estimation the time between his command and Unit 01 moving in accordance took approximately .843 seconds. Unfortunately he didn't have time to work on that as the Angel was suddenly upon him, swinging its arm to knock the Eva aside.

Shinji blocked the attack, which sent jarring reverberation throughout Unit 01. Gritting his teeth he countered with a left hook, only for the Eva's fist to be caught in the Angel's clawed hand. The end of the arm started to glow and an energy lance rushed forward and pounded against the hand's armor. It pulled back and pounded forward a second, third, fourth time.

To Shinji felt like his hand was being smashed by a hammer. Not needing the distraction he shut off the pain receptors within his left arm. At the same time Unit 01's shoulder pylon opened and the Eva grasped the one weapon in its arsenal, a single progressive knife.

The progressive knife was a weapon with a blade oscillated at an intense speed, giving it cutting power strong enough to pierce the hide of an Angel. It wasn't much, but it certainly caught the Angel's attention as Unit 01 drove it into Sachiel's shoulder.

Sachiel roared in pain, breaking away from its attack and backing off slightly. Shinji took the opportunity to drive Unit 01's fist towards the vulnerable core, but the effort was for naught as his attack slammed into the unyielding force that was the Angel's AT Field.

'Damn it! Getting though that barrier is going to be a real problem without enhancements.' That's when the Angel's eye's started to glow with a familiar power. "Oh Hell." Deadpanned Shinji just before the blast struck Unit 01, sending it flying backwards half a kilometer before it crashing into a building and effectively demolishing it.

Shinji groaned as he struggled to get the Eva back onto its feet, only to knocked down by a second blast, with a third, fourth, fifth, and sixth right on its heels. The force of the explosion dazed Shinji for a few seconds. Coming around he suddenly felt stabbing pains in his legs that threatened to put him under again if he didn't shut off sensation to them. A quick assessment told him that both legs had broken ankles where the armor was weakest as well as some long twisted piece of rubble piercing the back of the right knee. The left arm was a mess, the weakened armor having shattered completely, revealing the Eva's organic nature. And as if that wasn't bad enough the rest of Unit 01's armor was riddled with stress cracks from the multiple energy assault.

Bringing his attention back to the Angel, Shinji saw that it seemed satisfied with the damage it had inflicted upon Unit 01 and was back to blasting through the armor plating that protected the Geo Front.

'No! If it gets to NERV its all over!' He shouted mentally. "Damn it! Move!" He commanded the wounded giant, which shuddered upward for a moment only to slump forward "I need to protect the city! It's my purpose to fight the Enemy! I need to protect this world from the Enemy!!"

Unit 01 heard its pilot's cry and it responded, for it had the same purpose. The mighty titan's head snapped upward, its eyes blazing with power. The jaw restraints snapped apart like wet paper and the Eva released a mighty roar to the Heavens. Lowering its head Unit 01 saw its prey.


With a gasp Shinji's eyes snapped open. Confusion overtook him for a second as he took in his surroundings. As the confusion ebbed away and clarity set in, Shinji settled down. The room he was in was a standard hospital room, probably run by NERV.

His gaze shifted upward as he let his thoughts drift, the sound of cicadas in the background. Aloud he said, "Unfamiliar ceiling."


In another portion of NERV, within a room behind the cavernous expanse of the Commander's office that is off limits to all but Gendo Ikari a meeting was taking place. A meeting between Gendo Ikari and the five members of the Human Instrumentality Committee, the UN officials in charge of overseeing NERV and adjusted the budget based on the organization's performance.

In truth it was all a sham. The UN may be the ones who are officially in control of NERV, but that was only in name and on paper. When it came to dealing with NERV the UN was just a puppet, and the puppet master was the organization SEELE. The secret benefactors of the Katsuragi expedition, and who later would provide the stimulus needed for the creation of GEHIRN and manipulated who would be selected to be on the Human Instrumentality Committee. The members of SEELE were unknown and their goals a mystery to all but a handful outside their number.

It was in this meeting room where the Commander debriefs the UN about the confrontations between NERV and the Angels. As usual the discussions did not go well. It was only to be expected when such men were thrown together.

SEELE didn't trust Gendo, but at the same time they realized that they needed him. Gendo suffered the 'Old Men' because they had the resources he needed to accomplish his goals and at the same time had the resources to remove him if he ever lost value in their eyes.

It was an exhausting dance, and a lesser man would walk away from it looking years older. But Gendo Ikari merely looked annoyed as he returned to his office and sat down at his desk.

"How did it go Ikari?" Asked Sub-Commander Fuyutsuki who appeared from the shadows at Gendo's side.

The Commander sighed as he adjusted his glasses. "They threatened to cut our budget."

"Do you think they will?"

"Unlikely sensei. The Old Men know now that the Angels have appeared they cannot take any risks with the scenario. And taking away our money when we need it would do just that. No they will wait until repairs have been made to Unit-01 and the city, just to show us that we are still on their leash."

"Hmm." Mused the old teacher as he pulled out several documents. "We have the preliminary results on the Magi's analysis of the Third Child's synchronization ratio."

"Thank you sensei." Said Gendo, taking the papers, then setting them aside in favor of other matters.

Fuyutsuki raised an eyebrow in confusion. "Aren't you going to read it? You did ask for it."

"Later. I already knew that the Third Child would be able to synch with Unit 01 at a much faster rate than the First and Second Child can with their Evas. I just did not expect it to be so great. So while it is an anomaly, it is minor and warrants little attention. And I doubt the cause of the anomaly is anything that will negatively affect the scenario."


Shinji stood in a window lined hallway with NERV Medical. His gaze swept over the lush forest that surrounded the small lake that filled the Geo Front. Again Shinji couldn't help but wonder at the majesty and grandeur of the manmade cavern.

'Or is it manmade?' A frown graced his lips as Shinji considered the needed logistics To construct everything he has seen in the past twenty-four hours, and it simply didn't seem feasible.

Tokyo-3 was hardly a new city, having formerly been Hakone, but it had been considerably modernized and militarized since Second Impact. Then there was the construction of NERV's facilities and defenses. And finally he had to consider the Evangelions. They would have needed a considerable length of time and money to be built and tested.

Doing all that while at the same time digging out several cubic kilometers of earth, then undertaking a major landscaping endeavor to replicate the outside world? The costs of such projects would be staggering and probably be more time consuming then everything else, and the landscaping that created the lake and brought in the vegetation served no practical purpose aside from aesthetics. 'But what if NERV merely dug their way to what was already here…'

Shinji's musing was cut short as he heard the sound of wheels. Turning he saw that it was Rei. "Excuse me nurse," he called to the woman pushing the hospital bed. "Would you mind letting Ayanami-san and I talk alone for a minute? I'll even take her back to her room for you."

The nurse had no problem with it and acquiesced to his request. When she had left Shinji took her place and pushed the bed along to its destination, while studying its occupant. Outwardly he noted that the First Child still wore bandages in all the same places as she did yesterday, and she seemed mildly confused at Shinji's request but ultimately uncaring. However inwardly Shinji was trying to establish contact with the nanites in Rei's system. A task that was proving to be rather troublesome. 'The nanites I injected were programmed to shut down once their objective was complete, but from the looks of Rei's condition their mission was far from over. So why can't I get in contact with them?'

During his musing Shinji couldn't help noticing that Rei had yet to take her eyes off his face. "Do I have something on my face?" He asked.

"Why?" Asked Rei. "Why did you refuse to pilot Evangelion, and then accept to?" To Rei it was puzzling that anyone associated with NERV would refuse an order.

"Well technically I never refused to pilot the Eva. I was merely pointing out that the odds of a teenage male successfully piloting something as complex as the Eva for the first time when he didn't even know it existed several minutes before, against a creature that the JSSDF couldn't even slow down without the use of an N2 mine, were not good. I also asked what would happen if I refused to pilot. My father decided that he would demonstrate what would happen and called you in." Explained Shinji. "As for why I chose to pilot, well my reasons are my own." Shinji figured that Rei was the type of girl to be satisfied with such an answer, and she was.

However today something was nagging at Rei within her mind. "I remember something, before I lost consciousness. You said that you were keeping me safe."

'She remembers that!' "Like I said Rei, my reasons are my own. But yes I did pilot to keep you safe. It was clear that if I did not they would have made you pilot the Eva. And you were simply in no condition to do it. I can't even believe that they would even consider a plan that had a 100 percent chance of ending in your death."

"It does not matter. I am expendable." Rei said emotionlessly

"Don't say that!" Shouted Shinji so emotionally he jostled the bed, causing Rei to wince in pain. Shinji took some deep breaths and calmed down. "I'm sorry Rei. But you shouldn't say that. You shouldn't feel that way." His voice lowered and his eyes closed as memories from the past were called up. "That's how I felt years ago. I felt that I was useless, that I didn't have any worth. That if I suddenly dropped dead know one would care. And to be honest that could very well have been true. I had no purpose, nor was I anything special." Shinji's head picked up, his eyes opened, and his voice lifted with a bit of emotion. "But four years ago my perspective on life changed. When that happened I no longer thought of myself disposable. And I couldn't be happier because of it."

Rei was intrigued. The Third Child had thought the same as her in the past yet no longer did? Although she knew that Shinji did not know how if she died then there would be another to replace her thanks to the numerous spare clones kept in Terminal Dogma, nor that she was currently the second incarnation of the First Child. But still she couldn't help but wonder what it was that changed him. And she asked Shinji this as he pushed her bed through her room's door.

Chuckling Shinji responded, "Sorry Rei, but that would be my little secret. Maybe I'll share it with you someday. As for what I learned, well that is something you will have to experience yourself."

As Shinji said this he moved to stand on Rei's blinded right side to maneuver the bed into position, and has he did so Rei felt a slight prick so small that she wondered if it was just her imagination.

"Now Rei, I do believe you need your sleep." Rei registered these words as her eyelids grew heavy and sleep overtook her.

Shinji watched as the unusual girl fell asleep. Someone as injured as she was really needed to get plenty of rest, but it didn't hurt that his nanites were helping to induce sleep. 'Now then, let's get to work.' Keeping a hand on Rei to help insure there were no communication errors, he sent out his nanites to figure out the girl's secrets and what had happened to the first group.

Within 15 minutes he had found all of the deactivated nanites of the first group. It was odd because he found that they had begun repairs to Rei's body, and it was because of those repairs that Rei was even conscious today. Annoyed at the lack of progress he immediately ordered several of his nanites to bring back some of the deactivated machines.

Once several specimens were returned Shinji ordered a standard breakdown and memory dump. Across his eyes data images appeared. In his left eye were the images of the breakdown process and the examination of every single almost molecular sized component that made up each cell-sized machine. In his right eye was a detailed report on Rei's physical makeup that the original group had gathered before deactivation. For the most part it was pretty standard. She did have some odd pigment cells in her eyes and hair, thus giving her the unusual colors. Rei could also stand to have more protein in her diet. That's when a list of her organs and their conditions popped up and Shinji's eyes nearly bugged out of their sockets.

'What is this!?' He mentally shouted in surprise. 'It's impossible! This can't be right!' Yet there it was. Most of Rei's organs were the same as any other persons, except for one. It was her womb, or rather her lack of a womb. In its place was another organ that shouldn't exist in a human, only in the Enemy or as NERV calls them Angels.

He didn't know what NERV called it, nor did he really have an equivalent word in Japanese or any other language he knew, but the race that built the nanites called it a sisione. And it was a very interesting feature of the Enemy, even more interesting than their core and barrier.

From the dissected bodies of the few Enemies that had been killed mostly intact came the discovery of the sisione which was the source of the Enemies power. Or to be more precise it was a source of virtually unlimited energy. If it could ever be replicated it could be used as a devastating weapon. However the enemy seemed to know that and raided the site the first one captured was being studied. After that anytime a body of the Enemy was captured dead yet intact, it would decompose too quickly to be of any use to anyone.

'Yet here is one perfectly intact, if seemingly not functional, within a human.' Shinji then frowned as he suddenly remembered Unit 01 which was an Angel without the sisione. 'So is she truly human?' He wondered. To answer that question he pulled up Rei's genetic profile and gave it a quick scan. The results made him do a double take. 'If I am reading this right, and I do believe I am, then Rei, as impossible as it sounds, is half Angel.' This was getting to be too much. Incomplete Angels, human/Angel hybrids, giant 'manmade' caverns, and fortress cities. 'I need answers. But first…'

Shinji immediately began recalling the nanites in Rei's body. Once they were returned to him he would begin reprogramming them. Because she was only half-Angel the nanites wouldn't try killing Rei, however she was just Angel enough that they wouldn't help her either, at least not now that they know what she is. But after a day or two connected to the main computer (his brain) they would then be ready to be returned to Rei to finish repairing her. And maybe once he got his answers, do more than just repairs.


"You'll be living alone?" Said Misato unbelievably.

It was later that day and Shinji had been discharged from the hospital. Currently he and Captain Katsuragi were going through the process to changing Shinji's residence from the house with his teacher to a place here in Tokyo-3.

A NERV official answered in the affirmative to Misato's question, stating that Shinji would be living in the sixth block of the residential district.

Shinji had no problem with it as it would allow him to work without interference, depending on whether or not he has to deal with any surveillance beforehand.

"Shinji are you sure about that?" Misato asked him.

Giving her a small smile Shinji answered, "Living alone is fine by me."

But it seemed it wasn't fine with Misato as minutes later she was on the phone with Dr. Akagi saying how Shinji would be living with her, as well as making several sexual jokes at his expense. Shinji though wasn't sure about it. He would be spending an incredible amount of time around his direct superior who presence could very well interfere his work. On the other hand his first and current impression of Misato didn't point towards a person who would be too troublesome to deal with. Perhaps he could even use her position to his advantage.

Hanging up the phone Misato turned towards her new ward with a big grin on her face. "Well Shinji it looks like you'll be bunking with me. And do you know what that means? A welcoming party!" She shouted excitedly.

Shinji smiled at the thought but he had to take care of some things first. "That's great Misato, but if you don't mind before we leave I'd like to visit with NERV's command bridge."

"Huh?" Was Misato's elegant reply. "Why would you want to see Central Dogma?"

"Well I just that that I should see the place that would be giving me orders in battle and to meet with the people I will most likely have the most involvement with." What he left unsaid was, 'And it will give me a great opportunity to leave some nanites to open the back door later.'

Misato didn't see any problem with the request, and began guiding him to Central Dogma. After half an hour and 12 wrong turns Shinji took the lead made two turns, took the elevator down three floors, walked fifty feet down a hallway, took another right turn, stopping in front of a pair of metal doors with the NERV logo underneath which were the words Central Dogma. And it only took 5 minutes.

Shinji looked back to Misato with a cheeky grin as he bowed and gestured for her to go first. Misato ran her ID card through the scanner and entered her password, all the while muttering about cheeky punks and labyrinthine buildings.

Upon entering Shinji couldn't help but whistle at the sheer immensity of the room. It looked large enough to hold an Eva.

"Impressive, isn't it Shinji?" Said Misato amusedly as she stepped forward towards several control stations where three individual in uniforms were working. One of whom had noticed the unexpected arrivals.

"What are you doing here Captain?" Asked the bespectacled one asked the Operations Director. "I thought your shift had already ended."

"It did Makoto." Answered Misato. "However my new ward here," she pointed to Shinji who had walked up beside her, "decided he wanted to see the place and meet your guys. Shinji this is Lieutenant Makoto Hyuga," she said pointing to the tech with glasses.

"Hey Shinji, welcome to NERV. And after last night I can gladly say it nice of you to join us.

"This is Lieutenant Maya Ibuki," this time indicating the mousy brunette and only woman of the group.

"It's nice to meet you Shinji."

"And the long haired rock-head is Shigeru Aoba," said Misato pointing to the long haired man with head phones on.

"Pleasure to meet you Shinji, and as a word of advice if you are going to live with the Captain you better know how to cook or else you won't be living much longer."

"What's That Supposed to Mean!?" Shouted Misato at the indirect insult.

Shigeru simply shrugged and said, "Let's just say your cooking is a little infamous to those who work with the technical division." In truth there were horror stories about Misato's collage days, most of which originated from a certain blond formerly brown haired roommate.

"My cooking is not that bad!"

"Maybe it isn't but better safe than sorry."

Shinji laughed at the sight of Misato on the verge of strangling her subordinate. 'Maybe I should divert their attention.' "It is nice to meet all of you. You three must have pretty important duties to work here."

"Yes we do Shinji." Said Makoto. "The three of us are in charge of running synch tests, monitoring the Eva and pilot during battle, assessing battle damage and making sure it gets repaired."

"Don't forget, Makoto, that we also in charge of monitoring the Magi, without which we wouldn't be able to do our job," added Maya.

This Shinji found intriguing. "Magi?" He asked the group.

It was Maya, the one with the best programming skills amongst the group that answered. "It's the Magi Super Computer System." She typed in a command on her council and called up an image of three turquoise squares connected by a ring with Magi in the center. "The Magi are three computers that utilized a sixth generation AI with the computers being named Melchior, Balthazar, and Casper respectively. The Magi run all of NERV's systems, and they're even hardwired into and control Tokyo-3's systems as well, so they in effect they 'govern' the city. They make decisions on what actions to take by voting between themselves."

"But weren't they built for the same purpose?" Asked a confused Shinji. "Then wouldn't they always make a unanimous decision?"

The question made Maya smile because it indicated that Shinji had a bit of knowledge about the subtleties of programming. "Normally that would be true Shinji, but each of the Magi was programmed with slightly different priorities, meaning that they each consider different aspects of any decision to be most important."

"I see," said Shinji. "It's an efficient system. Being computers they won't care about any outside factors beyond the pertinent facts. They can't be bribed or threatened. However computers are notorious for ignoring the human factor, and very willing to write off the deaths of a hundred if it saves a thousand. And they can be hacked. Granted I have no doubts that these computers have the most powerful digital defenses ever created on Earth. And a sixth generation AI isn't easy to fool. Fortunately I know a couple of non-Earth related tricks.' "Would you mind showing me the actual computers that store the Magi?"

"You already have," answered Makoto. "Right now we're all on top of Balthazar."

Eyebrows raised in curiosity Shinji walked over to the computer councils which were indeed the edge of a balcony that over looked the three massive computers. "Amazing," muttered Shinji as he quietly let out a horde of nanites. By themselves they wouldn't be able to do much in the Magi, at least not without being detected. But they did give Shinji a backdoor into the system, and that was all he needed.

"Yikes," said Misato as she looked at her watch. "C'mon Shinji. We need to get going if we want to get the supplies we need."

"Alright Misato. And again it was nice to meet you three."

Shigeru smiled as he said, "No problem Shinji, and remember my warning." He barely dodged the pen Misato threw at his head, laughing all the way at his superior's expense.


Fifteen minutes later Shinji learned a very important lesson. Misato didn't need a giant alien monster hot on her heels and the fate of mankind on her shoulders to drive with reckless abandon at insane speeds. No she was perfectly capable of doing that on her own.

Before going to Misato's apartment they made a couple of stops. The first to a convenience store where Misato bought her weight in instant foods and beer.

The second stop was a real delight as it was an overlook on a cliff where Shinji was treated to the grand sight that is Tokyo-3 coming out of battle configuration. The buildings rising from the ground like new growth was awe-inspiring.

What was equally awe-inspiring was the sight of the interior of Misato's apartment, but for a completely different reason.

"This place is a mess!" Was Shinji's obvious understatement when she opened the door. The floor and table top were littered with the empty beer cans, liquor bottles, trash bags, microwavable food trays, discarded chopsticks, cardboard boxes, and other items that were clearly meant to be thrown away, not to mention the stacks of dirty dishes in the sink. Stepping further into the apartment Shinji caught a glimpse of Misato's bedroom and while it didn't have the same contents as the kitchen and entrance, the floor was essentially blanketed in clothes, magazines, and more beer cans.

"Sorry about that, I just moved in myself and I haven't had the time to clean for a while," said Misato apologetically.

'Cleaned in awhile? Have you ever cleaned once since moving in here?' "That's alright Misato. Tell you what, why don't you cook dinner while I tidy up a bit?" He offered.

Misato's grin told him that not only did she agree but that she felt that she had won the lottery. "OK Shinji, but would you mind putting the food in the fridge while I change?"

"No problem," was Shinji's response. As his new guardian went into her room he opened up the first compartment of the fridge, "OK, we have ice." Closing the first he opened the second, "Here we have snacks," he said seeing the junk food contents. Finally he opened the third. "And this one is stocked with fifty galleons of beer. Honestly how can she live off this?" He asked incredulously. Then he noted the second fridge on the other side of the kitchen/dining area. "Hey Misato! What's the other fridge for?"

"Oh, don't worry about that, he's probably still sleeping."

"Sleeping?" Shinji shrugged. Misato probably had a pet for which she had converted into a pet house for. She seemed quirky enough to do just that.

Once he was finished putting the food away he started cleaning off the kitchen table and countertop, at the same time Misato came out of her room and her apparel almost gave the teenager a nose bleed. He had to admit that the picture he had received did not do Misato justice and almost made him wish that she was fourteen years younger. 'Oh Well.' He sighed wistfully while moving into the living room. He didn't want to accidentally catch Misato's attention while he went about his work.

His cleaning of Misato's, and apparently now his, apartment wasn't entirely altruistic. The reason he volunteered to clean the place was because while Misato was busy cooking it gave Shinji time to root around for items made up of useful materials. Shinji had used up a lot of nanites in the past twenty four hours and he needed to replenish his supply. He had a feeling, scratch that, he knew that he would be needing every last nanite available in the days to come. Even if they weren't in his body.

That was why he was cleaning up the place. Whenever he found something made of the appropriate materials he would either absorb into his body or set it aside for later. When he absorbed something his remaining nanites would break it down on the molecular level until only the base elements were left. All useful materials would then be stored for processing.

Shinji didn't find much in the fifteen minutes since he started to when Misato called him for dinner.

During the meal Shinji learned several more things about his guardian. One, her culinary skills seemed limited to microwavable instant foods and curry. Two, she drank an unhealthy amount of beer. Three, unlike for most people where alcohol acted as a depressant, for Misato beer seemed to act as a stimulant.

After dinner the two played rock paper scissors to divide up the household chores. Misato was pretty good but when compared to a guy who had enhanced visual optic cameras for eyes that could slow the visual perception of time, and a nanite enhanced physical speed she just couldn't compete. Even when she tried cheating, like him. But Shinji was generous enough to split the chores evenly; he just chose to give the ones he didn't want to Misato.

"You should take a bath." Decided Misato once the chores were divided. "You didn't have one while in the hospital and baths not only clean the body but the mind and soul as well."

"If you insist Misato." In truth Shinji didn't need to take baths or showers, not when he had billions of tiny little robots that could pick any detritus material off his techno-organic body. But he found soaking in warm water soothing.

What he did not find soothing, more startling really, was the sight of a penguin right when he opened the bathroom door. Shinji blinked. The water fowl blinked. Shinji stepped aside and made a 'please continue' gesture. The flightless avian gave a brief 'Wark' of thanks and walked out of the room. Shinji's thoughts on the matter were, 'Misato is an odd woman.'


His bath finished walked into his new bedroom, which had a piece of paper taped to the door that said "Shinji's Lovely Suite." Inside the room was small, but adequate for his needs. One corner had his futon already set up for sleeping; another had a work desk for school work. Either then that the only items in the limited space were a number of boxes, most of which were marked fragile.

Opening up the largest boxed Shinji allowed his facial muscles to lift upward in a satisfied smile. Within the box were two desktop computers and a single laptop. These sleek machines did not look anything like what could be found in any electronics store around the world, and they weren't. They had started out their life like that but once Shinji got a hold of them he immediately took them apart and began the process of modifying the hardware, software, and outer casing to his specifications, before rebuilding them.

If anyone turned them on they would go through the standard boot up process for their standard counterparts, but that was just a masking program Shinji created so that any unauthorized users wouldn't learn anything about his capabilities or the capabilities of his machines. That program was also the only part of the computers that could be electronically scanned, because the masking program was the only part of the software that was still compatible with binary computer code.

One of the many gifts the nanites had blessed Shinji with was the knowledge of a computer code that was a hundred times more powerful, yet could be stored in the same amount of digital space. This made his computers technically more powerful and efficient than any contemporary supercomputer, but the sheer processing power controlled by the Magi would make them a tough nut to crack.

That's where the nanites he left in the Magi came into play. They were programmed with a tracer program that would leave a trail in cyber space for Shinji to follow back, and should leave a crack in the security software that he could slip through.

Taking the computers out of the box he set them up on the desk top with a homemade monitor set up in between. The laptop Shinji set off to the side, he wouldn't be needing that yet.

With the computers set up Shinji opened up another box and pulled out a smaller box. Within the box were a number of small disks about three centimeters wide and a half-centimeter thick. He pressed one disk against each all where it adhered itself. He activated them and some basic information flowed before his eyes for a few minutes. When it stopped he was a little surprised, there were currently no electronic surveillance equipment within their working range. 'Even if there isn't any surveillance currently but I leave them up. Don't want anyone just sneaking in here and messing with my equipment without my knowing.'

The disks were an item of Shinji's own design, and were very handy tools, especially if someone wanted to keep their plans secret. Their first function was to sweep for anything like listening bugs and video cameras. Their second function was to monitor the area so that no one could enter the room and do anything without Shinji finding out.

The next item to be unpacked was a large plasma monitor about sixty centimeters long and forty-five centimeters wide. Using the same adhering technology as the disks Shinji placed the monitor directly opposite of his computers. This device was relatively simple, when turned on it would show a picture slide show, or if set right a psychedelic blending of colors normally only seen on a hippie's t-shirt. But like Shinji's computers this was just a mask. Its true function is to pick up any wireless signal, like satellite TV, a cell phone call, that sort of thing. It could also could receive a special signal from the computers which it could then display as a holographic projection which could be physically manipulated thanks to sensors in the screen (think of something similar to what Stark used in the Iron Man movie).

After setting up a few more devices Shinji was ready. Sitting down Shinji shut off the masking program, changing the screen from the background of an ordinary commercial operating system to a purple backdrop across which lines of sigils scrolled across. Closing his eyes Shinji pressed his palm flat against the screen and uttered two words. "Log in." Shinji could feel his consciousness transfer from his body to the realm of cyberspace.

Moments later he opened his eyes to a sea of data composed of purple sigils. His body had changed, still maintaining the shape of a human, but everything below his shoulders appeared to be made of lines of blue sigils. Satisfied that the transition from his body to cyberspace was a success he looked forward and gave his command. "Initiate gateway connection. Begin trace."

With those words an opening appeared in the data around him, through which he could see a tunnel through which green lines of binary code soared. Before his feet appeared a red path appeared. Smiling he stepped onto the path and his digital body suddenly rocketed forward out the opening and into the network of Tokyo-3.

His tracer program was fast and efficient leading him to a wall of red data that could give the legendary walls of Troy a run for its money in the size department. This was the security that protected the Magi from outside hacking. Shinji stopped to examine it, reading the ones and zeros like most people read newspapers.

'This is an impressive system. If I tried getting in the traditional way it would take months if I was trying to avoid detection. Brute force is out of the question, and it would take a considerable amount of time to crack the algorithms. Good thing I made myself a back door.' Reaching out Shinji touched a seemingly random byte of code, only for the green zero to turn blue and shift into one of Shinji's sigils. Touching several more bytes Shinji activated the code his nanites had spliced into the security system, opening a door in the wall.

Shinji smiled as he floated through the door. Once through the world suddenly changed from a sea of data to a replica of the Geo Front. Even his body had changed and he found himself in his plug suit. "Well wasn't quite expecting this. Most digital realms aren't nearly this complex. Kudos to the programmer."

By happenstance Shinji had appeared right next to the entrance of NERV. Walking down the corridor, passing programs in the form of faceless employees of NERV, Shinji wondered where in this labyrinthine building he would find what he wanted to know. 'Well if the inner workings of the Magi mirror the real world, then the most logical place would be Central Dogma. So I might as well start there.' With that in mind Shinji made his way to the control center of NERV, and possibly the Magi.

As luck would have it that the core of the Magi actually was in the equivalent of Central Dogma. And where Shinji found the first deviation from normal. A very big deviation. For in place of the control stations of the three techs he met earlier, there were three blocky, metal, throne-like chairs upon which sat three women. Moving closer to them he saw that each had the same face, brown hair, and a strong resemblance to a certain head of Project E. Although their style of hair and dress were quiet different.

The one on the right wore a skirt, button up blouse, and white lab coat with her hair cut short, much like the blond Dr. Akagi. The female in the middle wore a longer skirt, yellow blouse, and an apron and her hair was longer but tied up in back. Finally the woman on the left, and woman was an accurate description. She was dressed to kill in a little black dress with matching pumps, and her hair was as long as the woman in the middle but left down.

The three appeared to be sleeping with their eyes moving as if they were in REM sleep. As he took a closer inspection Shinji was startled when he saw that the woman weren't just sitting in the chairs but were hooked up to them.

Frowning Shinji extended his hand and a blue light shot forth shining on the woman. It only took a few minutes for Shinji to understand. 'Incredible! Those women are the core of the Magi. They are the programs which make all decisions and control everything. But these are far more advanced than a level 6 AI. They could be fully sentient. But those chairs. They're limiters. Clearly installed before activation or those gals could have shrugged off their influence. Now the question is do I want them to be fully aware? If they're grateful it could be a great benefit. Well here goes nothing.'

Extending his hand forward again another beam of light shined on the limiters, but instead of blue this one was red. However as he began rewriting code alarms started wailing and lights flashing emergency red came on.

"Warning Unauthorized Action Detected! Initiated Security Procedures!"

"Oh Hell!" Cursed Shinji. "Sorry ladies but it looks like we will have to try again another time!" He shouted as he sped towards the exit like a bat out of hell.


Within the real Central Dogma two techs looked over the screen as a message they had never seen before appeared. Limiter

"Do you know anything about program L-913920518 and why someone would want to hack it?" Asked one tech to the other.

"Nope, never heard of it. But whatever it is I think this alert is just a bug in the system. According to this the hacker was here in Central Dogma doing it and there's no one here but us."

"Hmm, guess we'll have to talk to Dr. Akagi in the morning."

Unfortunately for these two techs Section 2 was on their way to apprehend everyone in Central Dogma, by order of Commander Ikari.


Within 'Shinji's Lovely Suite' Shinji's eyes calmly opened as his mind returned to his body. 'NERV has a considerable number of secrets. Eva. Rei. The Geo Front. The Magi. And the Angels. It's going to take time to discover the truth behind them all. But right now it is late and sleep is an enjoyable activity when my body has to focus on nanite production.' With that Shinji got up from his desk, changed into some sleeping clothes, and plopped down on his futon, his mind entering sleep mode in seconds.

And then he dreamed. He dreamed of a race so similar to humans stuck in a seemingly endless war. Of giants clashing with titans in a battle of supremacy. Of purple haired race car drivers. And he dreamed of an innocent blue haired angel.


Author's Notes: OK I am going to be honest here and warn you all that I know little about how to program computers and accompanying terms so I am just making stuff up here.

Hope you all enjoyed the chapter.

Please Read and Review.