TRUE WAR

CHAPTER 02

BY WONGA316

COPYRIGHT AND DISCLAIMER

I don't own Neon Genesis or anything of its characters. If you want to use any ideas in the fiction just drop me an email – NOTES

This is my first attempt at a Neon Genesis fan fiction, so please be gentle. This scenario doesn't take into account the final 2 movies / episodes and Toji never lost his limbs during this activation.

Some of the guys may seem OC to the die hard fans. Sorry about this but I hope my ideas will make it worthwhile.

"…" Normal speech

'…' Thoughts

(…) Computer / phone / other chat (you will know what I mean…)

"Alright Kaji, I'll talk to you later." Ritsuko said as she closed her cell phone.

"Can I assume that Shinji didn't take to our plan very well?" Fuyutsuki asked.

"You could say that… It appears that Shinji has run away again." She replied.

The older man ran his hand through his grey hair. "This is awkward… I'll get Section Two to locate him" he said reaching for his cell phone. But before he could dial Section Two, it started ringing.

"Fuyutsuki here." He answered the call.

As Fuyutsuki spoke, Ritsuko's mind began thinking of changes to the plan with Shinji currently missing 'Rei should be able to fill in for Shinji until we find him but in her condition I don't think she would be to hold for very long.'

"What did you just say?" Fuyutsuki yelled suddenly, causing Ritsuko to jump. She had not expected quite an outburst from him.

"I'll be there right away." He finished and closed the call. Before Ritsuko could enquiry what had happen, The Vice Commander dialed his cell.

"Chairman Keel."

'What the hell? Why is he contacting the chairman?' Ritsuko thought as she tried to listen in on the conversation.

"I don't care if he's asleep. Tell him that she has returned from Unit One."

'What? It can't be… This does change things…' she thought.

"Sir, we have reports that Unit One has ejected a female person." Keel must have answered the call.

Fuyutsuki started pacing back and forth with an anxious expression across his face "Yes I understand." He closed his cell and ended the call.

"Ok… As you might have over heard, it appears that Unit One may have released Yui."

"What… This is unbelievable…" replied a stunned Ritsuko.

"Keel is going to meet us at the Hospital ward in about thirty minutes. We better hurry."

"What! He can't show up at NERV. I can't show up there either…" Ritsuko protested, knowing that Commander Ikari had pretty much signed her death warrant after destroying the copies of Rei for the dummy plugs.

"It's alright… It seems the chairman has a plan…"

KATSURAGI RESIDENCE

"Yes. What is it?" Misato reluctantly answered sounding tried and defeated. She was still coping with Shinji's departure and the last thing she needed was a phone call from NERV.

(Major. It's Hyuga. We have a situation.)

"Why? It's past midnight and Shin… What's going on? Is there an angel?" 'I better not let anyone know about Shinji yet… I may still be able to find him or he'll come back after a couple of days.'

(A women has been found in the entry plug of Unit One)

"WHAT? Did you just say Unit One has released Yui?" Misato screamed into her phone.

(What? Who's Yui?)

"Oh… Ah… Never mind, I'm on my way in."

NERV HEADQUARTERS – HOSPITAL WARD

"What the hell is going on Hyuga? It's past one o'clock and you call a priority three alert." Aoba complained as he took the seat next to fellow bridge member.

"Yeah and why are we here? If it's a P3 then shouldn't we be in the control centre?" Maya added.

A priority three alert called for all essential staff to be present. This included the bridge crew, the Major, either the Commander or the Vice Commander and the pilots. Being one o'clock in the morning Maya and Aoba were wearing civilian clothes and not their usually uniforms.

"I was watching the monitors as usually, when Unit One started playing up." Hyuga explained himself.

"What else is new? Unit One does that all the time. You didn't have to call P3." Aoba said little upset.

"When I checked Unit One, I found a woman inside the cockpit." Hyuga continued.

"What the?" His answer surprised Aoba.

"No… It can't be…" Maya whispered to herself but was over heard by Hyuga.

"Can't be what Maya?" he asked.

"Oh… Never mind…" she replied.

Then all of them turned their attention to the sound of running foot steps coming down the hallway. Misato rounded the corner and looked like Maya and Aoba. Her hair a mess and ever present NERV jacket all wrinkled.

"Where is she?" The Major asked a little out of breath from her running.

"The doctor and nurses are with her now. Commander Ikari has been in there since they pulled her out of Unit One." Hyuga answered the Major.

"I see…" She replied as she took the seat next to Aoba.

"Where's Shinji? A priority three requires him to be present." Maya instantly picked up on the absence of the shy and quiet boy. While Misato tried to thinking up an excuse for Shinji missing, the medical staffs were busy assessing their patient's condition.

"Her vitals are stable. What's her heart rate?" The doctor asked.

"It's steady and rising." A nurse replied.

The on call doctor and two nurses were summoned when the Hyuga notified them of the situation. It was usually a quite night in the hospital ward. Their only real patient was Asuka who was resting just a few rooms down the hall.

'How long is he going to stand there? It's starting to get my nerves…' the doctor thought as he continued checking the woman. Commander Ikari's presence was making him nervous and difficult to work.

"How is she?" Ikari demanded.

"Ah… she seems fine. All vital and readings are stable and normal. As far as I can tell there is nothing to be concerned about. She seems to be almost in a deep sleep." The doctor replied.

"I see. Leave and inform everyone that no one is to enter this room." Ikari ordered.

"Yes sir." The doctor complied. He finished his work and left the room with the nurses.

Gendo waited for the medical staff to leave when he pulled the visitors chair next to the bed and took his place by his wife's side.

"You've returned to me… Yui…" As the medical team filed out, Misato was still trying to piece together a convincing story for the bridge crew.

"Ah… Shinji… He's…"

"Is everything ok with Shinji? He isn't sick or anything?" Maya asked.

"Pilot Ikari is not feeling well and will not be available today." Rei stated. She had received the alert like everyone else and made her way to NERV as stated in the official procedures stated. No one had noticed her arrival since they where busy discussing among themselves but young pilot always had the uncanny ability to appear when she was not expected.

"Oh… I hope he gets well soon." Said Maya.

Rei choose not to sit with the adults but stand beside the door. Misato looked up to the young albino girl and nodded a discreet thank you. Rei responded with a small nod herself. Their interaction went unnoticed by the bridge crew.

"LET ME GO…" Everyone peeked up when they heard a woman yelling inside the room. The scream was more of a demand than a plea for help.

"Yui… Please clam down…" Gendo pleaded as he struggled to keep the woman in bed.

"CALM DOWN! You bastard let me go! Where's Shinji? I want my son! WHERE'S SHINJI?" Yui demanded as she tried to force her way out of bed. She had ripped the IV line that was attached to her arm and knocked the bag to the ground causing its clear content to spill all over the hospital tiles. The monitoring equipment began beeping erratically.

"Yui… you have to rest." Gendo pleaded again 'I've never seen her so upset… could this be a side effect from the EVA?'

"I've rested long enough! I know what has been going on here, you bastard! You can't hide anything from me. I have to find Shinji!" She screamed again.

"What's going on?" the doctor asked as he entered the room. The alarms from the monitoring equipment had a direct feed to his pager. Any changes in a patient's condition could be sent to the doctor immediately alerting him of any possible danger.

"She's in shock from the EVA extraction. Give her something to calm her down." Gendo ordered still trying to hold Yui down 'Please forgive…'

"You fucking liar…" Yui screamed at Gendo.

The doctor hurried to the medical cabinet on the opposite side of the room and returned with a syringe. In his rush, the door was left open and everyone could see what was occurring inside.

"Major, help me restrain Yui while the doctor gives her the injection." Gendo had notice her sitting in the hallway. She hesitated and wondered what to do. Gendo saw the hesitation and spoke once more.

"THAT'S AN ORDER, Major."

Misato complied and entered the room. But when she saw the look in the mother's eyes she stopped. All she saw was a sadness and longing. Most of all Misato saw Shinji.

"Misato help me… Please… I have to find Shinji…" Yui pleaded almost crying. Misato was almost brought to tears herself 'Her eyes… so sad… just like Shinji's…'

"WHAT ARE YOU DOING MAJOR?" Gendo demanded. "GIVE HER THE INJECTION, DOCTOR!"

The doctor had also stopped in his tracks after Yui's plea to find Shinji.

"THE INJECTION YOU FOOL!" Gendo yelled as he reached over and ripped the sedative from the doctor's hand. He was about to penetrate Yui's vein when someone grabbed his arm and spoke.

"That's enough Commander." Rei said sternly as she held Gendo's arm, which had the needle.

"Rei!" Yui and Misato exclaim at the same time.

Rei didn't know why she stopped the Commander but it felt right. She didn't care if she was disobeying orders or the consequences that might follow. Something inside her heart told her that it was the right thing to do 'I'm unsure if this is correct but I know the pilot Ikari would do the same…' she thought.

"Useless shell of the child!" Gendo muttered as he swung his arm that Rei was holding and knocked her to the ground forcefully.

"Rei! Are you ok?" Misato asked with concern in her voice. She bent over to help Rei off the ground. Maya had also rushed to help Rei

"I'm… fine… Major…" Rei replied, favoring her back and a little out of breath.

"YOU BASTARD! DON'T TOUCH HER!" Yui demanded. She managed to get one leg and placed a well timed kick to Gendo's mid section. This sent the Commander back a few yards from the end of the bed. Yui saw this as an opening and quickly sat up and started removing the remaining tubes and wires that were still connected to her body. The doctor saw this and decided to act.

"Miss you should really rest. We still don't know what your body has been through. It's best to take things one step at a time." The doctor said trying to persuade Yui to remain in bed.

"I know you have good intensions doctor but I have to find my son." Yui said in a calm voice.

"Yui…Please…" Gendo said getting up off the ground.

"Please nothing you piece of shit. You expect me to listen to you after everything you have done to my son. YOU KILLED ALL THE HAPPINESS IN SHINJI'S LIFE!" Yui said, yelling the last part.

Gendo was taken back by Yui's outburst. He never would have conceived Yui could ever react to him like this.

"Ah… Miss Ikari… I think the doctor is right… I can bring Shinji to you." Misato said with hesitance since she was unsure if it was Shinji's mother and the fact that Shinji was missing but at less it would give her sometime to sort things out.

"Listen Misato… I'll explain everything after I see Shinji. I haven't held my little boy in nearly 12 years… you have to understand… do you know what's it like to not hold your own child for such a long time" Yui said, hanging her head low, try to hide the tears that threaten to spill again.

Yui's words hit Misato hard. During his time at Tokyo 3 and NERV, Misato looked at Shinji like the little brother she never had. Since her father's death, Misato had been alone all her life until Shinji arrived. Shinji never judged her for what she did. He would look the beyond the NERV uniform and found the true Misato inside. She made sure Maya was ok with Rei before walking over to Yui and helped her out of bed.

"Let go find Shinji" Misato said to Yui. She looked up and saw the compassion in her eyes. Yui nodded accepted Misato's help.

"It's been a long time Yui…" someone said from the hallway.

Everyone looked towards the voice and found Kaji, Ritsuko, the Vice Commander and another older man.

"Kaji? Ritsuko? What are you doing her? And who is this? Misato asked gesturing towards the older man standing next to Fuyutsuki.

"It's alright Major… He's with us." Kaji said nonchalant. His laid back attitude during certain situations angered Misato.

"This is no time games Kaji!" She said sternly, still supporting Yui with one arm.

"I believe we have not had the pleasure of meeting, Major Katsuragi. I'm…" The older said but Yui finished him off.

"…Lorenzo Keel…" she whispered.

"Chairman Keel? What are you doing here?" Gendo demanded.

Keel ignored Gendo for the moment and continued walking towards Yui and Misato.

"It's been a long time Ms Ikari… But I think the doctor's suggestion is the wisest choice. I'll bring Shinji to you and take care of everything. You just concentrate on resting." Keel said as he held Yui by the shoulders.

"…But Shinji…" Yui protested.

"I know, but you all the time in the world… everything will come full circle. Please be patience." Keel said.

Yui slowly complied and was helped back into bed with Keel and Misato. The doctor approached and started reconnecting her monitoring equipment. The nurses began cleaning the mess made.

"Agent Kaji, would you please escort Commander Ikari to the holding cells for the time being." Keel asked the pony tailed man.

"With pleasure…" Kaji replied as he approached the Commander flanked by two other men dressed in uniforms that differ from Section Two.

"Sensei? What's going on?" Gendo asked looking at the Vice Commander.

"It's over Ikari. I wouldn't resist if want to see Yui again…" Fuyutsuki replied sadly 'Not that Yui would want to see you again…'

"Don't touch me. I can walk on my own!" Gendo spat at Kaji and the guards "You traitor! You've been with SEELE all along. How could you betray me?"

"I didn't betray anyone Ikari. You did the betrayal. Yui and Shinji suffered because of you…" Fuyutsuki stated as Kaji lead Gendo away.

"…His name is not Ikari… its Roubu…" Yui said before succumbing to sleep. Gendo had heard Yui's comment and turned to face her only to find her asleep. Leaving the room, Gendo thought about Fuyutsuki's and Yui's words. He slowly realised that they were right. All of his actions to date have been for himself and it had cost him his family. He didn't look at anyone as he was being led away, knowing that he would have the rest of his life to ponder what went wrong or where he went wrong.

"It might be best if we let her rest for now." Said the doctor. Everyone complied and exited the room, leaving the doctor and Yui. When everyone was outside Keel addressed everyone "I suggest everyone go home for now. We'll continue this tomorrow when everyone is rested and cleared their minds…"

"But Shinji is still missing!" Misato said, interrupting Keel.

"What? Rei didn't you say the Shinji was sick?" Aoba asked the young pilot. Rei didn't respond and only hung her head. There was no point hiding the fact any further. Misato produced Shinji's letter and handed it to Keel.

"I didn't expect this…" Keel said after finishing the letter. He passed it onto Aoba who was shadowed by Hyuga and Maya. When they were done reading, he passed the letter back to Misato.

"We have to go look for him." Hyuga said.

"And where would you start? Remember this is Shinji we are talking about it. He managed to slip from Section Two for a whole week when he first came to NERV." Ritsuko stated. Everyone knew that she was right, if Shinji wanted to disappear he could.

"Look… I'll get my men to start searching for him. In the mean time I think we should keep this from Yui. I don't want to upset her any further." Keel said to the group. Everyone agreed.

"If all works out, he'll be located before Yui knows that he has run away." Fuyutsuki added.

NERV HEADQUARTERS

The next morning everyone assembled in the planning room. It was clear that no one got some actual rest last night.

"Since everyone is here we can start…" Keel said, motioning to Maya who sat at one of the terminals controlling the wall and floor projections. Maya brought up a portion of security surveillance tape from train station yesterday morning. It showed Shinji waiting in front of the indicator boards and then leaving with his bag.

"That's Shinji!" Misato exclaimed.

"Yes. This was taken yesterday at Tokyo 3 Central station. My agent found that Shinji boarded a train destined for Old Kyoto yesterday morning." Keel said.

"I suggest we make arrangement for Old Kyoto as soon as possible." Rei stated in her monotone voice.

"Just a moment, Rei. We checked the tapes at Old Kyoto and couldn't find Shinji leaving the train or any trains during the day." Said Keel.

"That doesn't make sense. We have tape footage of him getting on at Tokyo 3. What does this mean?" Misato added.

"We are still not sure. Tickets collected at Old Kyoto indicate the Shinji never got off there, which mean that he some how manage to get off the train before or after Old Kyoto."

"We have to widen the search." she said.

"Keel, why are you so interested in finding Shinji?" Ritsuko asked.

"What the hell are talking about Akagi? This is Shinji we are talking about!" Misato yelled across the room.

"Misato, I'm not saying that we shouldn't find Shinji. I don't want anything to happen to him either. It's just that SEELE is spending a lot of effort to locate just one boy." Ritsuko counted.

"They are a few reasons why I want to locate Shinji. He has given so much to this world and asked for so little in return. All he wanted was a normal life. I want to repay his sacrifices and reunite him with his mother." Keel said.

"But that's not all, is it Chairman?" Ritsuko asked.

"You are right Dr. Akagi. I believe that the Angel war is not over as stated in the Dead Sea Scrolls and we need Shinji's help." Keel replied.

"WHAT! Shinji killed the last Angel. What do you mean the war is not over?" Misato demanded.

"Major! You are out of line." Fuyutsuki said sternly.

"Screw you! You bastards have been hiding the truth from all of us. Do you know what Shinji has to go through to save all of us?" Misato yelled as she pointed at Fuyutsuki and Keel.

"It's alright, Fuyutsuki. Major Katsuragi has ever right to be upset. I don't want any of these children in these machines fighting for mankind but we have no choice. We have not been hiding the truth from you because the fact is that we don't know what the whole truth is." Keel stated.

"What do you mean?" Kaji asked.

"Large portions of the Dead Sea Scrolls have faded due to time and decay, making the translation process difficult and a long process. We don't even know if the translations are correct but I believe Dr. Ikari can help us fill in the blanks." Keel replied.

"Dr. Ikari? You mean Yui, Shinji's mother?" Misato asked.

"Yes as you know the angels are called that because they are the Messengers of God. Yui is only the second person I know that has returned from direct contact with these Messengers."

"Messengers of God… Then that would mean…" said Huyga.

"Yes. The EVA Units are Angels themselves or to be more precise copies of the Angels."

"Who would be the second person?" Misato asked Keel

"Shinji… " Keel's response caused a pause in the discussion.

"I believe since you people know Shinji the best, I'll leave the remaining search up to you. You have SEELE'S full support and any resources that you may require to complete the task. Fuyutsuki will assume Ikari's role as Commander." Keel finished.

"Thank you, Sir" Fuyutsuki replied.

"I'll break the news about Shinji to Yui…" Keel said before being interrupted by Misato.

"No… I'll like to do that… I mean requesting permission to inform Dr. Ikari on Shinji's status." Misato said in her NERV voice.

"Of course… Major." He had no problem with her request. "I'll be leaving later today to update the other chair members on what has occurred. Feel free to contact me if you have any questions or concerns." Keel finished. Everyone agreed and watched him leave the room. After he had left Fuyutsuki addressed the group.

"Starting from today I'll like to promote Ryoji Kaji to head of Section Two. I believe that there might be a few Gendo aligned men there that we need to weed out and if anyone can find Shinji. Does anyone object to this?"

Kaji acknowledged and no one protested with Fuyutsuki's decision.

"Everyone else is to remain in their positions and continue with their work as planned. Any questions?"

"Who will be the Vice Commander now that you have been promoted?" Rei asked.

"I'm not sure Rei… Let's just concentrate on finding Shinji for the moment, with current data from the Dead Sea translations, an angel attack is highly unlikely therefore we can afford to be short staffed for temporary."

"That's right. The MAJI have only estimated a 0.01 chance of an Angel attack in the next month or so" Maya added from the terminal.

"Unless there is anything else you are all dismissed." Fuyutsuki finished

HOSPITAL WARD

Misato walked towards Yui's room. She wondered how she would explain Shinji's leaving to Yui 'What I'm I going to say? How do I explain to Yui what happen to Shinji?' Misato was too busy thinking that she failed to notice Rei waiting outside Yui's room in one of the waiting chairs.

"Rei…? What are you doing here?" she asked slightly surprised by the albino's appearance.

"I like to see if Dr. Ikari's recover is proceeding well." She stated.

"You know you don't have to be at NERV now, you can go home if you like." Misato replied 'I'm not sure how Yui is going to react to Rei's presence…'

"Oh… Morning Major, morning Rei." The day shift nurse was leaving Yui's room and interrupted their small conversation.

"Good morning. Is Dr. Ikari awake?" Misato replied to the nurse.

"Yes. I have just brought her breakfast. You two can go in if you like." The nurse answered. She held the door open and motion for both of them to enter. They walked in and saw that she was awake and currently enjoying her breakfast.

"Ah… Good morning Dr. Ikari…" said Misato hesitantly. Rei remain silent as she followed Misato into the room.

"Oh… Excuse me…" Yui said wiping her mouth with a napkin.

"It's alright… that must be the first breakfast you have had in a while." Misato responded, trying to make light of the situation.

"You're right there, Major. Oh… Good morning Rei, I didn't see you there." Yui replied, noticing Rei quietly standing behind Misato.

"Good morning"

"So… Misato where's my Shinji?" Yui said cheerfully, moving the breakfast table away.

"Ah… Yui, there is something that I need to tell you. It's about Shinji…" said Misato as she took the visitor chair next to Yui's bed.

"What's wrong? Has something happen to Shinji?" Yui asked full of concern. Misato responded by handing her the letter that Shinji wrote before he left. Misato and Rei looked on as Yui read Shinji's letter. They notice the tears starting to flow down her checks.

"Kaji has been promoted to head of Section Two and is currently leading the search for Shinji." Misato said sadly.

"I have to find him…" said Yui as she started to get out of bed.

"Please Dr. Ikari, you have to rest. I know Kaji will find him. It's not going to do Shinji any good if you exhaust yourself trying to find him." Misato pleaded to the distraught mother.

"But he's out there all alone… I have to see him… I have to hold him…" Yui said half crying and still trying to get out of bed.

"Dr. Ikari, you should rest. No harm will come to Pilot Ikari." Rei stated.

"Rei… What do you mean?" Yui questioned the young girl.

"I'm unsure but I have this feeling that Shinji will return to us." Rei replied.

"But…" Yui protested.

"During the Angel attacks Pilot Ikari always returned when we needed him. I believe in my heart that he will do the same in this instance." Rei finished.

Misato was shocked that Rei was holding a semi conversation with Yui. During her time as Major she had only seen the albino girl speak a few words. When Misato thought about it more, she realised that it was Shinji that Rei would normally speak to, even if it was just a few words. Even more surprising was Yui, she stopped trying to move after her words.

"… I can see why my Shinji likes you…" Yui said, wiping the tears from her eyes. The older woman's comment brought about a light blush from the young girl.

"What do you mean by that?" Misato asked Yui.

"As you know I was part of Unit One. Whenever Shinji would synchronise with the EVA, I would be able to feel his feelings, see his memories and his thoughts. He cared deeply for both of you and Asuka." Yui said sadly.

"I see… can I ask you did Shinji think of me?" Misato asked.

Yui smiled at the Major and replied, "You know how Shinji feels about you, Misato. Though, he was concerned about your drinking sometimes"

Misato laughed a little at this before saying "Thank you, Dr. Ikari… I just feel somehow responsible for Shinji's leaving… I feel… I don't know, may be if I had been a better guardian, someone who would be they for him…" Misato had started to shed some tears herself.

"No Major, You're wrong. Shinji saw you as family. You were there from him. I should be thanking you for taking care of my Shinji while I was away." She said trying to cheer up the Misato.

"Thanks… I can see where Shinji gets many of his traits from…" Misato wiped away a few of her tears.

END OF CHAPTER

AUTHOR'S NOTES

Thanks to all that reviewed (both positive and negative)

I'll do my best to try and weed out all of the grammar and spelling mistakes but guys know what I'm try to get across ;)

Just to let you know Shinji will not be making an appearance for a few chapters. I want to set the scene for our hero to return with a big bang.

For Auska fans, she'll be making more of an appearance in chapter 3.

BTW – this is a cleaned up version. No changes made to the story line. I only cleaned up the glaring mistakes I missed previously.

Wonga316