A/N: reuploaded it after finding some errors
Answers:
ANON: Some punctuation would really help people understand your comment. Having said that, you're right. Commander Ikari has no idea that it's Rei doing the rebelling.
Kaiser: Define 'going well'...
Fanus: Okay, that makes sense, but I do like hearing your opinions rather than summaries (Everybody can summarize a chapter. Opinions are unique and insightful)

Disclaimer: See Prologue
Chapter 19: Terror

"Mr. Ikari, do you know where Miss Ayanami has been?" The old schoolteacher asked at the end of the day.

"Uhh, yessir. She's been having to go to regular checkups lately." He lied, not daring to risk Rei's trust in him. "I don't know what she's going in for, but she's not skipping school."

"Very well, these notes need to go to her address. Everyone wish her a get well soon and have a good evening." He turned the class over to Hikari who handled the afternoon's duties.

"Rise, Bow, Class is Dismissed. All right, Touji, I promised you would have next cleanup, and you've got it. You can handle today's delivery as well."

"Seriously?! Hikari, why have you been picking on me lately?"

"Because you have the attention span and obliviousness of a newt. Get going!"

"I can't just show up at a girl's place, especially if I barely even know her! Shinji, will you go with me?"

"Yeah, sure, if it'll calm you down." = I hope she's home safe. I hate my father and Ritsuko just for thinking about that LCL chamber. =

"Thank you, Shinji, you're a great friend." Hikari complemented him as she left.

"'Attention span of a newt'?! Since when has she been so snotty?!" Touji asked as they walked through the building projects towards Rei's building.

"Maybe it's because she wants you to notice her." Shinji considered. Hikari and Touji were obvious to everyone except themselves.

"Look, if that's what it's about, I could ask her out whenever I want. I just know we'd have a shitty first date, and worse second one!"

"You know, I thought the same thing about Rei."

"Except that you told me yourself, Ayanami doesn't do 'dates' or stuff like that."

"Exactly. We just spend time together doing the normal stuff we need to work on."

"That doesn't work for me. Hikari doesn't like sports and I would pull my hair out if we just did homework together."

"Do you know you're sounding more hopeless than I am?"

Misato was standing over Ritsuko in her office.

"Unit-03 just landed in Matsushiro. What's the status on the Fourth?"

"I just got the report from Marduk."

"Then why haven't I seen it?"

"Here, read it now, if it'll make you shut up!"

Misato looked at the folder and gasped. "HIM?!"

"As it turns out, he matches the newest core and is already known to have a good relationship with our active pilots."

"Sure, that doesn't discount the fact that he just happens to go to the same school as the current three. How convenient that must be."

"That was on purpose. The Marduk institute has all potential pilots transferred to the same high school class in order to provide security and quick access."

"I don't like that reason, but it makes sense. I'm not worried about Rei's reaction, but don't tell Asuka or Shinji. Asuka will probably goad him into killing himself, while Shinji would have a breakdown at another of his friends being put in danger."

"Yes, I agree. It pains me to see the psychological weaknesses of our pilots preventing them from melding into a real team." = We won't have that problem, soon. =

"If I have to blatantly order them to accept Touji when the time comes, I'll do it." = If only to try to keep you from defiling Rei's mind any more. =

"Why would Ayanami want to live in a place like this?"

"I've asked her that before. NERV lets her live alone, but this is the only place they'll give her." That answer only made him hate what NERV had put her through even more.

They went up to the fourth floor, Shinji started opening the still-broken door. = How much work does it take for my father to order a repair crew out here. Does he even care about her at all, anymore? =

"Yo, Shinji, you don't just barge into a girl's apartment without any notice!"

"It's okay Touji, I have permission and I kind of know where she is right now." = We should be sparring in afternoon training, right now. But building those disgusting dummy plugs is more important to my dad. Bastard =

"I still don't like it. Man, it looks a little better from the inside, but the place is falling apart!"

"It was in even worse shape when I first met her. There's not much she's been able to fix, so she just puts up with it." = At least she's been keeping it clean. Maybe my explanation motivated her..."

They deposited the papers and turned to leave as Rei walked into the room.

"Shinj-...Pilot Ikari, Suzuhara," She lapsed back into her formal, impersonal language. "How long-"

"It's okay, Ayanami. We've just been a couple of minutes. We needed to drop off your class notes. Shinji's told us you've been at the doctor's office a lot lately, everybody in class hopes you get better soon."

"...Shinji, how much did you tell them?"

"Just that you had to be at your checkups, Rei, you know I don't know why they make you go so often." He winked at her while Touji wasn't looking.

= Then he has not revealed anything true about me...this is good news. = "Yes, thank you, Shinji. Thank you for bringing my lessons, Suzuhara."

"Hey, just Touji, okay? If you're close to Shinji then you're my friend too..." The two boys left, Shinji smiling towards her as they walked out.

= I thanked...Touji. Before now, he was a stranger. More and more I dislike rendering false stories to the individuals I approach. =

"Miss Katsuragi!" Ryouji bowed to her as Misato entered the break room, "Allow me to express my gratitude to you for your efforts. The report is on its way to the United Nations as we speak. Word's out on whether it gets reviewed before the next Angel decides to finally show up."

"Ugh...not likely. Well, it's time for payback, Kaji: What's the deal with the Marduk Institute?"

"Three words: Wet. Toilet. Paper. They don't even actually exist. NERV has been hand-picking the pilots the entire time."

"Then how do they match the pilots to the Eva Unit?"

"I don't know yet, but I do know that it doesn't just have to be NERV doing it. While I was in England, I was the bodyguard for the Unit-05 pilot. I protected her before I was assigned to Asuka. She doesn't even report to NERV, she works directly for the UN. I'll be introducing you to her soon."

"...Unit-05 was destroyed-"

"In order to cause a blackout at Bethany Base, it was external sabotage. And the motivation for it is what I'm investigating. You never heard of any of this, but I have a feeling the sabotage order came from the Commander."

"There's three sides now, Kaji. NERV, the Commander, and Ritsuko; the Pilots; and you, me, and apparently your English frien-"

"When we're able to reveal ourselves to the Pilots, there'll be two sides, and the side with the Pilots will be the winners."

"Tell me this, Kaji, what's your motivation? You could just as easily be turning all this information to the Commander for a hefty reward."

"If I were motivated by money, I'd have been a rich man a long time ago. I'm in this now for my selfish desire to know everybody else's secrets."

"...If you're able to save these kids from whatever NERV is planning for them, I may just tell you a few of mine in the future."

"I look forward to it, Beautiful."

"Rise, bow, break for lunch!"

The kids in 2-A all broke into their respective groups. Asuka and Hikari sat down together, Shinji tried a meal that Rei had prepared in her small kitchen, and she was a better cook better than Misato was, at this point. Touji and Kensuke left for the cafeteria as Touji was called into the principal's office, where he met a tall, blonde woman wearing a lab coat.

"Touji Suzuhara. 10Th grade basketball player, right?"

"Uhh, yeah...Do I know you, or something?"

"Not quite, I'm Dr. Ritsuko Akagi, head of research and development at NERV. I've been reading up on you and you happen to be our best fit for our newest Unit."

School was dismissed as Touji stayed behind and started wolfing down junk food he bought as lunch ended.

"Touji! You should have been cleaning the class, not wasting time!"

"Look, class rep, I don't eat often. I missed my meal today, and I'm trying not to keel over."

"Don't you eat at home?"

"No, my sister's still in physical therapy and my dad works two shifts now. We never see each other. Nobody cooks, so I just take advantage of the school cafeteria."

"Oh. Touji, I'm sorry, you're always so cool and confident I never knew you had any difficulty with anything..."

"It's alright, I'll get to work soon."

"...Let me help, if only to apologize..."

"Uhh...Thanks Hikari..." = Maybe it's because she wants you to notice her. = "Listen, have you been talking to Asuka, recently."

"She saw you talking to Rei outside..."

"That's because she and Asuka already know, I haven't had the chance to talk to Shinji about it..."

"What?"

Touji closed the door to the room.

"We've got absolutely nothing in common, but I do really like you, and that's why I'm telling you this. Maybe because you're so good at being a leader or whatever. Can you keep secrets?...I mean real ones."

"I don't know, how 'real'?"

"I'm going to be working with Shinji, Rei, and Asuka."

"What do you mean 'working'?"

"NERV's Unit-03 is here, and somehow I've been picked to pilot it. I've never done anything military-like in my life, and now I'm going to be fighting alongside Shinji...I punched him when he first moved here because I blamed him for Sakura getting hurt...he made me look like an idiot for it, and now..."

"You have a chance to make it up to him."

"I only agreed to do it if they gave Sakura personal care and rehab...I'm still scared shitless because of it...Shinji hates piloting it, Askua's a complete psycho- even if you two get along -and Rei's always in bandages or casts because of it...I don't know how they do it. Don't tell anybody I told you this stuff, it's classified..." He tried to keep a straight face and broke down laughing at the absurd turn of events. "I've never thought I'd tell anybody that 'it's classified'."

"If it's that important, why are you telling me?"

"Because I needed to get it off my chest and Shinji already left; he and Rei are probably off staring at each other somewhere..."

"Maybe that's what helps them handle it. Nobody understands what they go through except them...You will, soon. Would you have been allowed to say no?"

"They let me set a bunch of terms for them and stuff before I agreed..."

"Then you still said that you'd do it. That's really brave of you, whatever happens. Just think about it, you're helping to protect the entire world! I'm really proud of you, for what it's worth-"

Hikari felt herself get squeezed in the boy's strong hug. "It's worth a lot, it really is..."

She hesitated for a minute, the realized her arms were around him as well.

"I have to leave tomorrow to start testing in it. I don't do much, just learn how to turn it on and walk around..."

"Oh my! Kaji is guarding us tonight!" Asuka jumped into his arms as he walked into Misato's apartment.

"Asuka, you make yourself look immature whenever you do something like this. I know that you have more self-respect than to try to seduce a man twice your age."

"What is wrong with you, Kaji? What do you see in an old bag like Misato?"

"Someone who understands adult economics and adult worries."

"I understand all of that! I'm a college graduate!"

"And Miss Ayanami is essentially a high-school graduate, but she has far more maturity than you act like you have. You all still go to high school classes because you can be protected ther-"

"How the hell do you know what Wondergirl does?!"

"I have access to pilot records. She is almost as well-educated as you are. Technically, Shinji is the only one in the proper grade, but he already makes better decisions than you do."

"Kaji, why are you treating me like this?" She pouted to him.

"Because if you want to act like an adult, you're going to be spoken to as an adult. You never listened to me when I was trying to raise you in your parents' absence, and now Misato gets to essentially have a vacation from putting up with you. Now, it's late, you can have first choice on the washroom, I need to speak with Shinji."

"Fine." She huffed and stormed into the bathroom.

"I wish I could change her past, but it seems I can't even change her present...Shinji!" He called into the boys' room.

"Yeah, Kaji, what do you need?"

"Just a moment to discuss a few things...That means you'll have to turn off the music for a few minutes."

"Okay, fine." He walked into the living room.

"I know you won't like either of us, but we're on your side."

"Who? You and Misato?"

"Exactly." He laughed a bit and continued. "I'm honored that you consider me a father figure."

"...When did I say that?"

"A few nights ago, when Miss Ayanami was here with you."

"...How the hell do you know about that, Kaji." Shinji was suddenly very angry.

"Misato heard everything, and we're working on a plan to stop the experiments and help Rei, but we need you to make it work."

"How did Misato find out?"

"With her ears, Shinji, it's not that difficult, you know."

"You two betrayed Rei's trust!"

"And we're going to use that betrayal to bring down the dummy system. Rei won't be a walking lab report anymore. She'll get to spend all her time with you; maybe she can learn to be an actual teenage girl for once."

"How?"

"You'll know when the plan is implemented."

"You two still betrayed her. You expect me to trust you now?"

"We didn't want to tell you earlier, but it looks like we've got no choice. Misato wouldn't say anything because she thought you'd panic: Touji is the Fourth Child. Unit-03's pilot."

"...What?! He can't be! He has no ties to NERV whatsoever! He shouldn't be put in this madhouse no matter how much NERV 'needs him'!"

"You're absolutely right. That's why we're doing all of this." He handed him a miniature portable radio. "Carry that wherever you go. It uses an entirely different spectrum than what NERV operates. When the time comes, you'll get a message from me. Rei will be on board after a while, I promise you. Asuka still needs time to see what's going on."

"If I help you, what do I do?"

"What you do best. Tomorrow you'll be on full alert while Unit-03 is tested. Kick ass in your Eva Unit."

Misato and Ritsuko were in the bunker at Matsushiro Air Base. A temporary Eva storage frame had been erected outside and Touji had been flown in on a NERV VTOL.

"All right, Candidate Suzuhara, the startup walkthrough should appear before you. Is your headset secure?"

He adjusted the antennae worn over his forehead. "Yeah, I guess they are...Is this manual like a hologram or something?"

"Very good, it is. Read the instructions then radio in to have us begin the activation from our end."

"Okay..." = Read, Touji...Facilitate A-10 connection, I guess that means the headset...Twin joysticks and triggers, right in front of me...view screens, all around me...call for external startup... = "Okay, it's Suzuhara. I've read the instructions, I'm 'calling for external startup'!"

Ritsuko's voice called over the radio to the facility. "All personnel! Unit-03 Activation! Repeat, Unit-03 Activation! Begin A-10 Neural Network Connection! Detach Restraining Bolts! Attach External Power Supply!"

Touji felt like he grew 50 feet tall as he sensed the Eva's body through the headset. The massive scaffolding frame dismantled itself, and the Eva Unit was plugged into the power cable...until it automatically ejected it.

"Why didn't it take the power supply?!"

"Ma'am, the Unit is rejecting the Pilot's neural interface as well as external commands! It's going beserk somehow!"

Unit 03's blue and gray armor became covered in a spiderweb-like fungus. The now-independent beast roared and generated a massive AT-field in a sphere around it.

"Lieutenant Colonel, the AT-Field is absorbing some kind of energy...Oh my God it's-"

The field expanded in a massive explosive shockwave, the energy the Unit absorbed ripping the vicinity to shreds. Unit-03 began an ungainly walk from the remains of Matsushiro Air Base to Tokyo-3 and the GeoFront.

"What do you mean 'it exploded'?! Bring Unit 00 and Unit-01 online. Retrieve the Second Child and bring her to standby. Load dummy plugs into all combat-ready Evangelions!" Commander Ikari was watching the events unfold from NERV's command bridge. Katsuragi and Akagi were casualties in that explosion; he lost his two best advisors in the same moment.

Maya spoke up during the Commander's order. "Commander, the dummy plugs aren't ready for combat! The MAGI haven't been able to render any combat predictions!"

"It doesn't matter. With this threat, there can be no risks taken, and that includes the mortality of our pilots."

"...Yes sir." Maya knew for a fact that this was going to end poorly. Call it a woman's intuition.

"Commander, Unit-03 appears to be generating some form of fungal matter. It has integrated itself with the Eva's nervous system."

"General Order: From this moment, the Evangelion designated Unit-03 will be referred to as the 'Twelfth Angel'!"

Shinji and Rei were sitting at separate points on the expected path for the 'Angel'. Unit-02 was still in headquarters waiting for clearance from Germany to launch, if the German government would get around to allowing it. = Damn those European Bastards! = Asuka thought as she sat in the tube, not allowed to go anywhere.

Hyuga made the final report. "Unit-00 will have first visual contact. Unit-01 will be moved to its position to provide assistance. First Lieutenant Ayanami will report when contact has been made."

Rei waited in Unit-00 looking out for the figure on the horizon. Shinji waited severl kilometers closer to NERV HQ, waiting for his permission to move to Rei's position.

"Commander, I have a video feed of the Angel. I can confirm that it has the appearance of Unit-03." Rei's emotionless voice masked her newfound ability to feel fear.

Shinji spoke up, this time. "Can anybody see the entry plug?! What happened to the pilot!? What happened to Touji?!"

"The plug looks undamaged, First Lieutenant Ikari. Once it gets in range of our communications, we will eject it and the pilot can be rescued." Hyuga offered the only good news of the day.

"Rei," The Commander returned to giving instructions, "bring Unit-00's AT field to maximum and engage the target at range. Unit-01 will be arriving to provide combat support."

"Yes, Sir." She moved out from behind her rock outcropping and raised her rifle as the possessed Evangelion sprung from its walking path and jumped high towards Unit-00, falling and landing directly on top of it. Rei groaned at the controls as she felt 66 metric tons of the demonic beast crash down on her. It held its hand over Unit-00 and began to melt, droplets of the parasitic Angel beginning to infect Unit-00.

"Sever the left arm. We cannot allow Unit-00 to become contaminated by this...abomination."

"Sir, the pilot is still at the controls-"

"Do it."

Rei audibly screamed as her arm felt the sensation of being torn away from her shoulder. It took all of her normally unbreakable willpower to remain awake when her body wanted to black out to end the pain.

The Angel lost interest in Unit-00 and began to continue towards the city until it was intercepted by Unit-01, running at it's top land speed to reach Rei's compromised position. Shinji punched the Angel's body, only for the fist to deform and flex the elasticized body of Unit-03.

"What the hell just happened!? Maya! Send the Eject Signal to Unit-03. Get Touji out of here!" Shinji yelled as he looked the Angel in the eyes.

"Firing the plug...now!" The entry plug's rocket engines fired and lifted into the web of fungus, only to be trapped like an insect inside the adhesive material. "It's still inside Unit-03! Plug rockets weren't strong enough to rip through the fungus!"

"Dammit...Dammit, what do I do!? I can't hurt Touji!"

The possessed Unit's arms turned into a liquid rubber and stretched out to grab Unit-01 around the neck. Shinji felt Unit-01 and him being snapped back to face the Angel up close. Shinji began to reflexively wrestle with it as it was hit with a punch from Unit-00's remaining arm. The Angel sprouted two new arms and grabbed Unit-01 by the arms.

"No, Rei, you're in too much danger! Retreat now!"

"I will not abandon you, Shinji."

"You're not...abandoning me, you're protecting...yourself." Shinji said between gasps. " Now turn around and run!"

"...If you believe that I am so important as to remove myself from danger, I will do it."

"Yes, I do! Now go!"

Rei turned Unit-00 around and fled to her launch elevator. Shinji reverted to trying to break the four arms' choke hold on him, and felt himself beginning to lose oxygen from lack of LCL.

"Shinji," The Commander spoke to Unit-01 "focus less on the arms and get your knife into the Unit's core. It's the only way to stop it!"

"I...can't. Touji will be...killed.!"

"If you don't do it, you'll be the one dead."

"That's fine by me! I'm not letting...any body other than me...die today!"

The Commander scowled. "...The current pilot is too much of a risk. Activate the Unit-01 dummy system instead."

Shinji's controls shut down. He heard a grinding sound behind him as a column of mechanical equipment rolled over him and locked two arms and a new view screen over the original controls.

.seiceps ruoy fo srehto yb detanimod eb ot sa dniknamuh rof dab sa ton si em yb detanimod eb oT .edirp fo noitome eht si esol uoy llA .noisulli na si modeerF

Shinji couldn't understand the garbled language he thought he was hearing, but he could read the new view screen.

"...DMYSYS...? Is this what...they've been working on?...FATHER! Don't do this! It's not going to help anything!"

Maya spoke to the Commander. "Cross-sync confirmed, Sir."

"It seems to accept her, after all...send the order to begin the attack."

Unit-01 shot its hands around Unit-03's neck.

"NO! FATHER YOU DON'T UNDERSTAND WHAT'S ABOUT TO HAPPEN!"

Unit-01 crushed Unit-03's neck in its hands.

"FATHER! STOP THIS NOW! THE UNIT-03 PILOT'S DONE NOTHING WRONG!"

Unit-01 threw Unit-03 to the ground.

"THIS HAS GONE ON ENOUGH! STOP!"

Unit-01 ripped Unit-03's armor away and begin ripping the Unit's body apart with its teeth.

"TOUJI DOESN'T NEED TO DIE, FATHER! STOP THIS!"

Unit-01 chewed and spat out Touji's entry plug.

"FATHER! NO! NO! STOP! NOOOOOOOOOO!

The dummy system shut down, Shinji noticed that Unit-01 still had power...