Hey there! I made it to part three! Is that fast enough, or what? Thanks also to everyone who's reviewed. All of the reviews I've been given, well, at least up to the point I wrote this helped me immensely as either encouragement or things I've actually done wrong, or could have done better. Well, I'll shut up for now. I'll say more when I'm done. Oh and, by the way, this chapter is going to finally shed some light as to Shinji's past and his unreal tolerance to pain.

Disclaimer -- These things really are annoying… I can't think of anything stupid to write!

A.N.: "This is not a test."

'This is a test.'

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"What!" Ritsuko shouted at Misato. "What do you mean he's been missing since yesterday!" It was the day after the battle with the Angel and Shinji had not been seen since.

"I thought he was acting weird… but I never dreamed he'd run away." She answered.

"And you call yourself his overseer?" Ritsuko scolded her.

"Don't talk like that." Misato complained.

"We don't have much choice. We have to report this." Ritsuko said after a few seconds of thought.

"Wait! He still might…" Misato was able to say before being interrupted by Ritsuko again.

"If something happens, it'll be too late. Or are you saying that you'll go look for him yourself?"

"How?" Misato said sadly. "I have no idea… where he would go."

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"I'm home PenPen" Misato said as she arrived. She wandered over to where Shinji's room was and looked in. 'Hmm… I wonder if he's not coming home again tonight?' she thought to herself. 'Where could you have gone?'

She had a quiet dinner alone, and was taking a bath when she thought to herself, 'Maybe if I can figure out a bit of his past, I can understand why he left.' She got out, changed, and was turning on her computer when a loud knock sounded on her door. 'Who could that be?' she thought to herself as she went to open the door. To her surprise, it was two NERV agents who awaited her outside of her home.

"What do you want?" Misato asked the man directly in front of her.

"We are here under orders ma'am." The agent answered her in the no-nonsense way she knew them to be trained in. "We were told to inspect the Third-Child's quarters to try and find any possible clues which might lead us to his current location. Misato stepped aside as the agents got to work.

She led them to his room and watched what they did from the doorway. 'I can't believe that he started living with me nearly two weeks ago… His room looks almost the same as when he moved in. I can't believe he hasn't bought anything personal to at least try and change the room a little. She watched as one of the agents opened the door to the closet. Inside, another pair of the same black pants with white shirts that he always wore was hanging. She could also see several other pairs of shirts and pants lying intermingled with various bandages on the closet floor. As the agent tossed out the bandages, she notice that some where very bloody, some where cut up, and others looked extremely worn out. She had never noticed whether he was bandaged up at all.

While the agent in the closet was busy, the other looked under the bed. "What the…" he said as he reached under it. He pulled his arm out a few seconds later and clutched in his palm was a very small pill. It looked like a regular aspirin, and would probably been considered as such, if not for the agents examination of it. It looked white while looking at it in normal lighting, but when held up to the light, it had a slight reddish tinge to it. It was deposited into a small plastic bag and the investigation continued. The pill however, was the only thing of any interest that was found. The agents finished after about an hour and thanked Misato, who currently resided on the couch, on their way out.

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"You are to locate the Third-Child." A group of agents were informed several hours before two of them invaded Shinji's room. "He is to be retrieved alive if possible. He is also known to be violent, aggressive, and considered extremely dangerous. You are to take all necessary precautions if you intend to confront them. You two!" the one giving out orders pointed to two agents. "You are to search for any possible clues in the Pilot's home. That is all. Dismissed."

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'Glad that's over.' Misato thought to herself. 'Now where was I…?' She connected to the internet with her computer and began searching for relevant data about Shinji. 'Maybe I'll try finding about what the people that took care of him were like…' She looked first, for any living family members of the commander. She found nothing. She searched for people with 'Ikari' as a last name in the area where she was told Shinji came from. Nothing again. She kept at it for several hours again. Using resources that were available to her as the Operations Commander of NERV, she found absolutely nothing. According to all that she had found, the person who was supposed to have been taking care of Shinji for the past decade did not exist. 'What the hell does this mean!' she thought to herself. 'Is this a cover-up or something?' She thought to herself. She was about to give up when a news article in the site she had been visited caught her eye. "It was an old newspaper story about a murder. What intrigued her was that the victim's name was the same as that of Shinji's uncle.

It was about a man who was found dead in his home. The picture showcased was of the same individual listed as Shinji's caretaker. 'How can this be!' Misato pondered. 'How can he be dead when he was supposed to have been taking care of him up until a little while ago?' She scrolled upward to read the date of the issue and made a startling discovery. This report was over ten years old!

"What could this mean!" she thought aloud. 'Is it some kind of conspiracy or is his information just out of date. No one cared about him before he got here so an error like this is possible, but still… Something about this bothers me…

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"Ritsuko!" Misato shouted as she walked into the doctor's office. "I found something strange."

"Oh…?" She responded calmly, being used to Misato's entrances, she was no longer startled at her sudden appearance. "What a coincidence, I did as well."

"You did? What is it?" She demanded of her.

"No way. You came barreling in to my office so you talk first." Ritsuko said smugly.

"Oh fine…" She muttered before recounting what she had discovered.

"What!" Ritsuko said, taken aback. "What do you mean his guardian's been dead for the past ten years!"

"It's just that. I have no idea what's going on, but something about this seems very strange… So, what did you discover?"

"Ah yes, I almost forgot. Do you remember what the agents sent to your apartment yesterday found?"

"A small pill, right?"

"Yes. I analyzed it and discovered what it was."

"What it was?"

"Yes, it is medicine."

"What? Is he sick or something?"

"I'm not sure… It's not like anything that I've ever seen before."

"What's so strange about it? Medicine is medicine right?"

"Well, this pill that was found is extremely unique. It's composed of seven distinct parts. It seems they were compressed and placed in a single capsule." She said while pulling up a diagram on her terminal. The strange thing was one of the cores."

"What about it?"

"It seems to be a powerful painkiller."

"What? What would he need painkillers for?"

"I don't know…"

"Didn't you run tests on all of the pilots?"

"No. I tried to get him to comply but he threatened to cease piloting if he was not left alone. That's why I didn't even know about his arm until Rei told us."

"Rei…" Misato said. "That's another weird thing about him… Why does he seem to want to protect her so much?"

"I don't know… He does seem overly protective of her. I mean, he threatens to kill anyone who so much as thinks of hurting her… And, I'm not sure why, but I think that he really would…"

"He threatened you, right?"

"Yes, but I only said that to get him to fight… Still, I was almost frightened by his voice when he said it…"

"So what do we do now?" Misato asked.

"Nothing." She said. "All we can do is wait..."

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It was the middle of the evening and a figure glided through the tall grasses on the outskirts of Tokyo-3. This lone figure was soon intercepted by several others. The lone figure faced the group as one among the pack separated from them and walked forward.

"Shinji Ikari?" The lead figure said.

"And you are…?" he responded.

"Nerv Public Security and Intelligence Bureau. In accordance with clause eight of the Public Security Act, we are to escort you back to headquarters."

"Escort?" he asked while eyeing their weapons. "Don't you mean arrest?"

The man chose not to reply to that and instead said, "Will you comply?"

His answer was given in the form of Shinji's fist slamming into his face. The spray of blood and the sudden movement startled the other agents long enough for Shinji to deal with them. He slid towards the second and drove a palm-thrust into his chest. With the momentum of his strike, he spun around a third agent and back-fist punched him in the base of the skull. The fourth and final agent recovered soon enough to realize that with his three companions gone, he was on his own. As Shinji turned to face his final opponent, the man panicked and pulled the trigger on his weapon. The thunder of the fired weapon echoed across the vacant field as the rounds tore their way into Shinji's unprotected body.

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As Misato was preparing to go to sleep, she was interrupted by the sound of her phone ringing. Hoping it was news of Shinji, she rushed towards it.

"Hello?" she asked.

"Oh good," Ritsuko's voice came through. "I'm glad you're still awake."

"What happened?" Misato asked.

"Section-2 agents encountered Shinji a little while ago."

"What! What happened!"

"The four agents sent to retrieve him at the clearing on the outskirts of town are currently in Intensive Care."

"What? Why are they in the hospital? What happened to Shinji, Ritsuko!"

"They're thinking that they fought."

"The agents?"

"Yes, with Shinji. The agent's seemed to have been knocked out pretty fast but one of them opened fire on him."

"They shot an unarmed child!"

"Yes, they say that the agent who shot him is the one worst off. The other three should recover soon, but that one doesn't seem to be as lucky…"

"Wait! How do they know he was actually shot?"

"The group who discovered his location was more that four agents, however, they thought that sending the whole group would make him even less likely to comply. They said that they ran towards the clearing when they heard gunfire, but he was already gone. They found a trail of blood leading away from them but after an hour of searching, it was decided that he was gone."

"Oh no… what's going to happen to him now, Ritsuko?"

"It isn't good. He's being brought up on charges of treason and it's being debated whether he is more trouble than he's worth. In truth, I hope they don't find him. They might kill him if they do…"

"Unless he's already gone…" Misato managed to say in a small voice before hanging up on her.

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"Sir!" an agent reported in the commander's office the day after Misato's conversation with Ritsuko.

"What is it." He said.

"We have located and detained the Third Child."

"Where is he?"

"He is currently being held in Detention Block B."

"Very well. I shall be there soon.

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"Ugh…" Shinji said as he awoke. 'Oh man… What the hell happened…' he thought as he looked at his surroundings. He was not in any place he ever remembered seeing before. If he had to compare it to something it would be a dungeon. His arms were chained up to the ceiling and his body was forced to sit on the ground with his legs beneath him that were chained to the ground.

"Awake, are you?" the guard spoke to him. "Good. You have a visitor."

Before he had a chance to reply to anything the door opened and his 'Visitor' walked in.

'That bastard? He's lucky I'm tied up, or I'd kill him now!' he thought to himself but chose not to speak.

"Where did you go?" The commander demanded more than asked.

"What? Were you worried about me?" he said before the commander's slap snapped his head to the side.

"Answer my question." He said. When Shinji said nothing he was struck again.

"Where is you uncle." He asked.

"What? He's back where he lives." Slap.

"You lie. I never bothered calling him but I have been informed that he no longer lives. Why is that?"

"Heh… I killed him. Just like I'm going to kill you."

"What? When did you do this."

"When? Oh, about a half year after you left me with that bastard. Let me tell you, he hits harder than you."

"You killed him when you were five!"

"Yes. And as much as I enjoyed that kill, I know that yours will be all the more sweet…" He was about to say more when he began coughing violently.

"What is wrong with you?" he demanded as he saw his son begin coughing up blood.

"Isn't it obvious?" He said in a mocking tone. "I'm dying."

"What?" he demanded.

"Yes. That is why I left. I did not wish others to see my corpse."

"What is wrong with you?"

"You wish to know? Fine. I'm as good as dead anyway… I lied about killing my uncle. He is dead, but not by my hand, unfortunately enough… I was taken by some strange group who used me to perform even stranger experiments and in the end, this is what I became. I was given medication that was meant to stabilize me but I ran out a while ago."

"What happens without it?"

"Isn't it obvious?" he said before another coughing fit took him again. "I've got maybe one more day to go." He said with a lopsided grin. "After that, I'll go say hi to mom."

The room was quiet for several minutes before Shinji said, "If that's all then could you please leave because I'd rather not have your face be the last thing that I have to see."

The commander ignored his statement and decided instead to say, "Would you still be willing to pilot?"

"Hah ha ha… I wonder if you did listen to me… I'd be more willing to keep fighting if it wasn't for the fact that that I won't make it to the next attack…"

"Very well. I will inform doctor Akagi of your needs."

"Hey! Old man! What the hell are you talking about!"

Gendo's eyebrow twitched at being called an 'Old Man' and said "A pill of yours was found in your room. I will inform her that she is to analyze and reproduce them."

"What the hell?"

"It seems you are hard of hearing, child."

"Hey! Who the hell are you calling hard of hearing you old geezer! You're the one who probably needs a hearing aid grandpa!"

"You are to report to doctor Akagi after you are released. Afterwards, you may petition for a new apartment if you so desire." He said while facing away from him.

At the commander's order, the guards entered the room and untied him. They asked him to cooperate a bit longer seeing as Misato had expressed a desire to see him. He agreed and sat quietly until her arrival.

"Welcome back." She says as she walks in.

"Hey there." He says back.

"How does it feel to be back after having run away like that?"

"In truth? I feel like crap right now."

"No kidding." She said as she took in his appearance. "Let me ask you this, then. Are you still willing to pilot?"

"Of course I am." He said to a shocked Misato. "The fighting was never the problem. I had some things I needed to do and since I've been given an alternative, I guess I can keep going a little longer."

"Where are you going to stay?" she asked.

"Well, since I know that you were ordered to stay with me, I'll just look for an apartment or something and live on my own."

"I… I see…" She said quietly. He got up and walked towards the door. He was about to leave when Misato said, "You know… PenPen?"

"Huh…" he said, stopping.

"He… he was being used as an experiment where I used to work. They were through with him. I got him just as they were about to put him to sleep. Do you know why I took him in…? Such a useless, greedy bird?" She stopped for a few seconds then continued. "I felt sorry for him. There was that, but… well, I… I've always lived alone. I thought it might be nice to have someone who'd be there, waiting for me when I came home late at night, tired from work… I thought it might be nice to have a family. I… I'm not the kind of person who's got it together enough to live with a stranger just out of sympathy, or because it's my job. I didn't mean to do what I did. I am not your enemy Shinji…"

"Misato…?" he interrupted. "I'm… I am tired of being alone. I… I wish I could lead a normal life like everyone else but I can't anymore… please… can I stay with you…?"

"Shinji…" she said before smiling at him and saying, "let's go back… to our home, okay?"

Shinji looked at her, and gave her what had to be the first true smile she had ever seen on him before saying "Sure."

TO BE CONTINUED

How that? I really never meant to finish so fast, but I got a bunch of ideas in my head and I couldn't stop writing! For me, at least, when I write, I can see it playing out in my head, so, I want to see what happens. The more I write, the faster I can see what plays out. As such, work as fast as possible. Oh and, by the way, to the one that told me that I seemed to rush when I wrote, I give thanks. Without having to worry about finishing as fast as possible, I was able to write more calmly and I let the story flow instead of forcing it along. Oh, and if anyone thinks my story ideas are lame, then it's your own fault. If my ideas suck, it's because no one wants to give me any. I really do listen to what people say. I mean, damn, this whole chapter came from someone's suggestion to explain why I was making Shinji seem so tough. Seriously! Review and I will make this story the greatest I possibly can!

Later!