A/N: Hey everyone, before we start I have a little announcement to make: I've been thinking of commisioning some artwork for (Never) Alone Part 1 and 2. That said, I'm not super knowledgeable when it comes to Eva fan artists. If you have any reccondations, or think I should save it for after the stories complete, please send me a PM and let me know. Now that's done, lets dig into Chapter 3.

-Rollinaround


Evangelion

Gemini Rising

By Rollinaround

Episode 3

Brain Scan


Babylon. The city of rebirth. The star of the ocean. The last great city of man.

Floating above the sea, where the Australian continent once sat, Babylon was the headquarters of the United Nations, and the largest, most advanced city on Earth. In the years following the cataclysm, this place had become a home for the lost and the broken. The world capital was split into eight districts, each of them shaped like a triangle and forming an eight pointed star. In the centre of it all was the UN Headquarters, the seat of power that governed the lives of men and women across the planet.

Off the coast of Babylon lay a gargantuan fleet of battleships, spanning miles and miles of ocean between the city, and Japan. It was their first line of defense in the event of an attack from NERV. And attack they did.

Admiral Jones watched as his Advance Fleet was approached over a dozen A.I-controlled battleships. A formidable offense to be sure, but nothing that could hope to reach the city. "Hmmmph! They're testing us." Jones scoffed as NERV opened fire upon them. "Anything else coming, Mr Smith?"

"I can't say, Captain!" the young man said, typing furiously as a spray of gunfire grazed the hull. "They've scrambled our radar, and our sonar! Reports from the fleet are saying the same thing; we're fighting completely blind!"

The old man harrumphed as NERV's forces slowly beared down on them. "Well, if Gendo wants to see what this fleet is capable of, I say we give him exactly what he wants. Launch the jets!"

The sky was adorned with a streak of pure, white contrails as eight of WILLE's bombers soared above them, weaving around NERV's anti-aircraft weaponry with ease and dropping bombs on the ships' main cannons. With their weapons crippled, the Advance Fleet made short work of them, and only one ship remained above the sea. A destroyer, 200 feet in length, surged towards Jone's ship. It's weapons were naught but scrap metal now, but the steel sea monster powered forwards anyway. Bombs fell upon it's deck, missiles crashed into it's hull and yet still it sped on. "Impact in an estimated 47 seconds, Sir!"

"Fire the remote torpedoes!" the Admiral roared, "Get ready to detonate them on my mark, not a moment sooner or later!" A pair of long, black torpedoes shot from the underside of Jones's Ironclad. With no sonar to guide them, he would have to rely on his instincts. One second off, and he was a dead man. The old man closed his eyes, and waited for the moment of truth.

"Impact in 30 seconds!" Smith yelped as the ship dominated their view, "20 seconds! 15 Seconds!"

"Now!"

The resulting explosion blasted sea water into the air like a geyser, lifting the stern of NERV's destroyer, before it fell back into the water and began to sink. The crew breathed a sigh of relief as it slowly disappeared beneath the sea. The hull of the ship had already been ravaged, and that blow to the propeller was the final nail in the coffin. "Nicely done, men." said Jones, lighting up his pipe in celebration, "What's the damage?"

"We've lost 2 of our bomber jets." The Lieutenant announced. "3 battleships were sunk during the destroyer's charge and our aircraft carrier has taken severe damage to the starboard side."

"I see." the Admiral said, scratching his beard. "What of our submarines?

"We haven't heard back from them Sir."

"Nothing on the sonar either." Smith added, "We've managed to unscramble it, there's just no sign of anything below the surface. It looks like they were just, wiped out."

"Wiped out?" the Admiral sputtered, "But how?"

"I'm getting reports from the Second Fleet." the Lieutenant said, "Something's moving towards them at a high speed. It's not a torpedo, apparently; it's too big?"

"How big are we talking?"

"About a hundred and fifty feet in length sir."

The American man scratched his forehead. What kind of underwater craft measured a hundred and fifty foot long? Then again, maybe it wasn't a submarine. What if... "Oh no."

"Sir?"

"Tell them to drop the mines immediately!" Jones yelled, "Whatever you do, do not let that thing reach the city!"

Far below the surface, a long, white cylinder pierced through the sea, it's course set for Babylon.


It was a weird day for the people down in R&D. The introduction of a new co-worker was always a bit of an adjustment, but this one was downright surreal. Over the past 14 years, Shinji Ikari had gone from an everyday kid to a legend, a fable, a cautionary tale. Ask three people his story, you'd get four different tellings. People on board called him everything from a misguided hero to an out-and-out villain, and he'd been gone away so long, most people assumed he'd never be seen again. Yet here he was, in the flesh.

Mori the Receptionist was just about to close the Records Department for lunch, when the infamous Pilot stepped into the hall. The atmosphere of the room changed on a dime, the only sound in the room, his echoing footsteps. He wasn't what the Receptionist had expected. The boys had told him the boy seemed normal but very quiet, and was a dead ringer for his Father. Indeed he looked perfectly average at face value, and there was a clear family resemblance, but something about the kid seemed slightly off. There was just something about the way he carried himself, the look in his eyes and the dark bags hanging beneath them. He looked tired, and not just physically. On the whole there was just something, unsettling about this kid.

"Good afternoon." He said, bowing low, "I was hoping you could help me locate a file. Something called TE-027?"

"Um, sure." Mori replied, pulling up a list of the available files. He was slightly caught off guard by the boy's demeanour. He'd brought civilization to it's breaking point, and supposedly had the strength to bend iron, yet he was remarkably soft spoken. "Ah, here we are: Section Six, third column on the right. May take you some time though, that one's almost as old as WILLE itself."

"I see." Shinji said, bowing again, "Thank you for your help." All eyes were on him as he dug through the records, on the search for some obscure file from the late 2010s. Even knowing the file's rough location, each column was about 20 feet high, with thirteen shelves per column, each holding nearly a hundred different files. He was starting to think the whole thing was just a wild goose chase when he finally dug the thing from the back of Section 6. He jumped off the ladder, falling over 10 feet and cushioning his fall with his A.T Field. He stumbled to his feet, ignoring the weird looks he got from his coworkers, and left the hall without another word. And just like that, all the tension drained from the room.

On his way back, Shinji came across a young man, struggling to lift a supply crate off the floor. Normally, heavy equipment was carted from place to place, but in this case, the harness had broken and the crate tumbled to the floor. "Uh, little help?" the man asked, his eyes placed firmly on his work.

"Sure." the boy replied, lifting the crate into the air with little trouble.

"Holy shit!" the worker yelped, stumbling backwards as he and Shinji put the crate back where it belonged. "That's a hell of a grip you've got there man! What are you, half gorilla or something- gah!" The guy flinched in shock when he turned around and finally realized who was helping him.

"I'm sorry..." Shinji mumbled, shrinking back.

"No no, it's fine!" the man insisted, "I just wasn't expecting to see, well, you. Um, thanks for the help."

Shinji nodded silently. He knew the guy was just being polite, but there was no point in making a big deal of it. This was just the way his life was going to be. He took a closer look at the steel container. "To Lab 21?" he asked, reading the text on the side, "Never heard of that one."

"No surprise there." he was told, "That's where they work on all their top secret experiments."

"Really? Like what?

"Wouldn't be a secret if I told you." the man chuckled, "Besides, I don't even know myself, I just deliver the parts. We all have our own ideas on what they're doing over there but, we're not supposed to talk about it."

"Huh. Well have a nice day." As Shinji made his way back to Ritsuko's office, he contemplated the mysterious Lab 21 and what they were working on. When he thought of all the things WILLE might want to hide, especially from NERV, one thing sprung to mind, above all others.

Evangelions.

When he got back to the office, Ritsuko was waiting for him, along with Misato. "C- Colonel Katsuragi!" Asuka and Mari had advised him to follow military etiquette, and refer to officers by their rank.

"Good afternoon Shinji." the Captain said, "Sit down, please."


Misato watched as the former Eva Pilot was fitted with a Neuro Scanner, a small, cross-shaped gadget, lined with short metal prongs. Shinji winced as Ritsuko attached it to the back of his neck. Even with anasthetic, the experience was quite uncomfortable. "I'm sorry for this Shinji," Misato said, "If it's too painful, we can have the Scanner removed."

"It's fine." Shinji groaned, "I can handle it." He'd already consented to the experiment, and he'd suffered worse pain than this. The 7th Angel impaled him through both his hands. Compared to that, this was on par with getting his shots.

"This device will allow us to scan your mind on multiple different levels, in an attempt to locate, and communicate with the 10th Angel." Ritsuko explained, "Now the human brain is capable of processing multiple thoughts and emotions at once, so we're going to focus on one at a time, while blocking out the background noise."

"I understand."

"Before we begin," the Doctor said, "Perhaps you could tell us where you think the Angel is? Is it in your conscious mind, subconcious, Superego, Id?"

"I think it's in my conscious mind." he told them, "I can hear him speak to me, so that one makes the most sense. It's hard to say though, I don't exactly know how this works."

Akagi smirked at that. "It's not something they teach you in science class." she quipped, "Still, your consciousness is as good a starting point as any." She switched on a nearby radio, connected wirelessly to the Neural Scanner, and it came alive with about half a dozen thoughts, all playing at once. Ritsuko turned on a series of dials, drowning out the noise pollution while increasing the volume on specific trains of thought, one by one. They heard him question the legality of the device, a couple of songs from his SDAT player, a few nagging doubts, and then the radio went silent.

"There." Shinji said, "He's not saying anything but I felt him react."

"Can you hear me, 10th Angel?" Ritsuko asked. The feed remained silent.

"Come on Zeruel." said the boy, "They already know you're in there." Still no answer. "If you don't say something they'll think I've gone crazy so quit messing around." More silence. The Angel was on Shinji's last nerve. "Zeruel, if you don't speak up now I'll bash my brains out against the wall!"

There was a brief pause, before an unfamiliar, androgenous voice, echoed through the room. "Yes Lilin, I can hear you."

"Thank you." Ritsuko said, "We're going to ask you a few questions. Don't worry, it won't take long."

"I am unable to act on my own; I have all the time in the world."

"Good. First question, why did you leave Eva 01 with Shinji?" Ritsuko asked.

"I have not left Unit 01." was the reply, "I merely left a small piece of myself within the Lilin. The rest of me is back in the Evangelion. As for why, I wished to observe him. I could not comprehend the fact that one of your kind had beaten me, especially one as unremarkable as him."

"You expect me to believe that?" Misato asked, "You had no intention of merging with Lilith, or one of the Adams?"

"That was my plan, originally." Zeruel confessed, "But Lilith is in NERV's position, along with three of the Adams. I need either Lilith, or all four of the Adams, in order to achieve my purpose. And the King of the Lilin has his own plans for Final Impact, which I doubt will be to my benefit."

"Then what do you plan to do now?"

"I do not know." it admitted, "At present, I am content to merely survive."

"What about Shinji?" Misato demanded, "Asuka is suffering the effects of Angelic Contamination. If she's at risk of being possesed, then why isn't he?

"Or Unit 01?" the Doctor added.

"I can only speculate. If forced to give an answer, I would say that my kin has entered her in it's entirety. If left unrepressed, they would share an equal part of her mind. I am merely a fragment, leaving him the primary entity in this vessel." Ritsuko adjusted her glasses. It was difficult to tell if the creature was lying. "As for the Evangelion, I cannot take control. There is another presence keeping me suppressed."

"Wait, you mean Rei?" Shinji asked, hopefully, "You're talking about Rei, right?"

"I am not sure." the Angel replied, "It could be her, or the soul of the Eva itself."

Misato and Ritsuko shared a nervous gaze. Shinji would likely want to contact Rei. It was risky enough letting her clone talk to the First Child. If Shinji tried it, god knows what might happen.

"I believe that will be all for now." Ritsuko said, "Shinji, you may return to your room. Angel, we will communicate with you again soon."

The scanner was removed from Shinji's neck, and he was ushered out by one of WILLE's soldiers. "Captain." he said, turning to the woman who practically raised him. "I just want to say..." She held her breath, but the Shinji's courage failed him, and he ran out the door. "W- well bye!"

She exhaled as the door slammed shut. The Doctor gave her friend a knowing look, and Misato knew at once what she was thinking. "No, Ritsuko."

"I know you have some very good reasons." said Ritsuko as the Captain got up from her chair. "I don't like it either. But we're already in hot water, and if we don't take the necessary precautions..."

"I said no!" the Colonel yelled, storming out of the office.

Ritsuko sighed as she returned to her work. She was ashamed to have asked such a thing, but the stakes were gravely high, and every instinct she had told her it was a necessary evil. Still, to think they had to make such decisions in the first place, it spoke volumes about the state of the world.

The chains of duty weighed heavy on Ritsuko's shoulders. She couldn't imagine how it must have been for Misato.


"So, any of you see our "new arrival" recently?" Hideki asked, as he and the rest of the Bridge Crew sat in the Mess Hall, at a table specially reserved for them and the Eva Pilots.

"I passed by him on the way to work this morning," Hyuga said, biting into a hunk of spiced carrot, "But I didn't say anything. I don't even think he noticed me. He kept staring at the floor with this kinda blank look on his face. It was, kinda eerie now that I think about it."

Hideki looked unsurprised. "I saw him last night, coming back from the labs. The moment he caught sight of me, he looked away." The young man shook his head, "I think he was scared of me."

"That's something new." said Mari, who sat across from them with Asuka. "Someone else afraid of Hideki Tama." She and Tama chuckled over that.

Nagara was next to speak up. "I expect he's frightened by all of us." the Helmsman said, staring into her green tea.

"Ha, that's a good one!" Midori scoffed, "The hell's he got to be scared of? We're the ones at risk here! Meanwhile, he's sitting pretty downstairs, the Doctor went and gave him a job, and they're not even putting a choker on him!"

Asuka gripped her fork so hard she thought it was going to snap. The Radar Technician had a point, they were kind of throwing caution to the wind. But even when she was right, Kitakami had a talent for pissing everyone off.

"We did almost kill him." Koji pointed out, "And we've regularly treated him like a criminal. I think he has as much reason to fear us as we do him."

"He is a criminal!" Midori snapped back, "He killed almost ten million people, and the Captain hasn't done jack about it!"

Nagara took a sip of her tea, and a deep breath. "Put yourself in her shoes." the Helmsman posited, "Imagine you're expected to judge someone like that. This person has committed a serious crime, but they're also frightened, and confused, and their crime spawned from ignorance and good intentions. Now imagine that person is someone in your family; would you want to be in a position like that?"

Midori's eyes shot daggers at the woman. "Don't. Ever. Compare my family to him." she whispered, brandishing her fork like a dagger. Nagara stared her down for a moment, before returning to her drink.

Asuka finished her dinner as quickly as possible. She held her tongue; it was expected of her as an Eva Pilot, and she couldn't go around starting fights. Still, she had to leave soon, before she got herself court-martialled.

A short while later, Asuka and Shinji sat together in his humble bedroom. Mari joined them, in accordance with their Sync training, but the Second Child insisted she keep her mouth shut. "Fine by me," she had said, "Watching you two is fun enough on its own."

A fog of discomfort surrounded them. They hadn't really sat down and talked like this since Elysium, and they'd spent most of that time fighting with each other. "So..." she began, already feeling butterflies in her stomach, "How are you settling in?"

"It's going ok I guess." Shinji said, half heartedly, "The people at RD are nice enough, but I think they're scared of me. Every time I walk into a room I can feel them staring. The rest of the crew either ignore me, hate me, or... I don't know. The Vice Captain said I'll have to get used to it."

"You will." said Asuka, "It'll take a while, but sooner or later you'll stop caring, or they'll stop bothering you."

"The Princess and I put up with it for years." Mari said, throwing in her two yen, "But then, I think she scared them for other reasons." Her lips curled into that obnoxious, cat-like smile as her co-pilot shot her a dirty look. So much for keeping quiet.

"Aside from that," Shinji continued, "Work's been fine. Doctor Akagi treats me well, and I'm always kept busy. I never really know why I'm doing what I'm doing; everything's "classified"." he leaned back against the wall as he thought on his position. "It feels like she's keeping everything secret from me, because she doesn't trust me."

Asuka rolled her eyes. Did he think the world was out to get him? "You're just being paranoid, Bratty Shinji!" she said, "The Doctor keeps things from us all the time. lf it doesnt involve us, she's not gonna tell."

"Right." he said, "Sorry..."

"Don't be sorry." Asuka chided him, "Just, not everyone has it out for you." The kid averted his gaze. She could see there was something bothering him. "Anything else?"

"No..." he mumbled. It was such an obvious lie, it had to be a cry for help.

"You don't sound very convinced." said Asuka, nobody's fool but her own. "What happened?"

"Nothing." Shinji said, defensively, "I swear, nothing happened! Mph!" she gave him a punitive tap on the head. At times it felt like she had to treat Shinji like a child to get anywhere with him. But even a child needed discipline.

"Don't lie to me." she warned him, "If you don't wanna tell me, that's on you, but don't think I'm an idiot."

The boy stared at the floor as he explained himself. "Last night, Ms Suzuhara brought me here after work." he began, "I tried to apologise for what happened to Toji; what I did to Toji." Asuka could sense the tears were about to flow. "She, got really mad at me. She said I only cared about myself. She nearly hit me..."

Asuka inhaled deeply. That must have been very hard for Shinji, but then again: "Did she want to talk about it?" The boy shook his head. "You dumbass..."

"You think she was right?" Shinji murmured. Asuka struggled with that one.

"Maybe." she conceded. It was mean to say so, but he'd admitted to being selfish before. "I know you're sorry but..."

Mari cut in. "If you try to apologise, and she doesn't want to talk about it, it kinda looks like you care more about being forgiven." the boy tried to curl up into a ball, but Asuka stopped him, grabbing onto his arm.

"Don't do that." she said, "Just think about what you did, and what you should have done."

Shinji remained silent for a while. He had very little experience when it came to this sort of thing, so the answer didn't come easily to him. "I... I shouldn't have forced her to talk about it when she didn't want to. I shouldn't have tried to make her forgive me. I should have..."

"Waited." Asuka said, "You should have waited."

"Yeah..." Shinji said, finally, "So what should I do?"

Asuka opened her mouth to speak, but then caught herself. "I don't know." she conceded, "I've never really tried. I just did what I always did, and piloted Unit 02, and after a while, they left me alone. I never cared if they forgave me. Hell, I don't even know if they did." Shinji kept his gaze firmly on the ground. "But you're not like that, are you?"

"No." Shinji said, "I used to think I didn't care what people think of me but, I guess I do. It feels like everyone hates me, and it hurts..."

"Does Sakura hate you?" Mari asked him.

"I don't know..." he said, drying his eyes. "She said she didn't want to hate me."

"Well," Mari suggested, "Just sit tight, be good and try to do the right thing. Me and the Princess will help you with that. But don't do it because you want to be forgiven, do it because it's right."

"And if she doesn't forgive you," the Second Child added, "Well... she doesn't. I know it sucks, but that's how it goes sometimes." The boy's shoulders began to sag, and he hung his head in shame.

"Look at me." Asuka said, holding his chin up, making him stare into her one good eye. "Even if Suzuhara does hate you, even if she never forgives you, it's ok. You know why? Because you've still got people who care about you."

"It's true," said Makinami, "Me and the Princess still care, and Kensuke. Hell, I bet the guys in the lab'll give you a shot too. Just keep at it ok? I know you can do better."

Shinji smiled at them weakly. "Thanks." he whispered. "That helps, at least a little bit."

"No problem" Mari said, checking her watch. "It's getting late." she told Asuka, "We better get going before lights out."

"Alright," Asuka said, getting out of her chair. "I'll see you later alright?" Shinji nodded his head, keeping up his smile as they walked out the door. "Take care of yourself."

With that, she closed the door, leaving the boy alone once more.

'Damn it!' she thought, 'What the hell kind of advice was that?' she would have bashed her own head in if Mari wasn't there, not that it helped, as the girl seemed to have noticed anyway.

"I think that went alright." she said.

"I made him cry!" Asuka replied, "You think that's alright?" She buried her face in her palm, "It's hard..." she admitted, "I want to help him but I'm not his Mommy; I can't be there for him all the time."

Mari patted her friend on the shoulder, but she stepped away. "You don't have to be there all the time; you shouldn't. You can still help him, but some things he needs to figure out himself. Besides, it's not like you're the only one he has."

"I don't know," Asuka said, pulling her hat on, "I guess."

"And you didn't make him cry, he's just... delicate. Give it time, he'll toughen up."

The one-eyed Pilot rubbed her forehead. The whole thing was giving her a headache. The kid had fought Angel after Angel, and learned to take pain like a champ but this, this was something he didn't know hhow to cope with.

They almost made it back to the room when theur comm devices started beeping. "Damn it..." Asuka grumbled, "What now?"

The Colonel's voice came through, and she sounded panicked. "Mari, Asuka we need you to get down to the Eva cages right now! Babylon is under attack!" Mari felt a chill down her spine when she heard what they were up against.

"It's the Eva Series!"

And a few thousand miles away, the tall, green Evangelion, waded through the twisted remain's of the UN fleet, it's red eyes glowing in the night.