Disclaimer: This story takes place after Episode 26 of the series.  The movies never happened in this timeline.  The story, its original contents and ideas, and any original characters belong to the author and cannot be used or reprinted without the author's permission.  All other characters belong to their respective owners.

 

Genesis 1.01

Dark Dragon, Dark Ally

 

Outer space

 

            Fifty thousand years ago

 

            “AAH!  Don’t these bastards ever give up?!”

            “’Fraid not, buddy!” a voice replied over the comm. link between the two star fighters.

            As the pilot dodged another volley of laser fire, he saw the other fighter explode in a flash of light.

            “NOOO!” the pilot screamed, almost losing control of his own fighter.

            He looked forward again and saw a sphere of energy rocketing straight toward him.  He had just enough time to scream before the sphere hit, blowing the fighter into millions of pieces.

 

NERV HQ

 

            Present day

 

            “Crap.” Misato swore. “Not another one!”

            “What now, Katsuragi?” Gendo asked.

            “A large crater.  Can’t scan the interior.  Possible Angel landing.”

            “Where?”

            “A mile due north of the outskirts of Tokyo 3,” Misato replied.

            “Send Shinji and Rei.  EVA-00 should be repaired by now.  With Geo-front still flooded, we can’t risk an Angel attack.”

 

Outskirts

 

            “If this is just another meteor,” Shinji groaned over the comm., “I’m gonna be pissed.”

            “ . . . ”

            “This is becoming really irritating.  Over the last month, we’ve had fifteen meteor crashes.  Not one of them turned out to be an Angel, like Gendo thought.”

            The two pilots continued on ‘til they reached the crater.  They climbed the slope and looked down into the crater.  What they saw was no surprise.

            “Great.” Shinji moaned. “Another empty crater.”

            “Churahk kou ne?” a voice called out from behind the two EVAs.

            They quickly turned to see a large humanoid creature.  Only it had wings, a serpentine neck and tail, and a Velociraptor-like head.  It’s skin was solid black with a few silver highlights.  A ring of horns crowned the back of its head.  Two blades stuck out from each of its forearms, the ones closest to its wrists pointing forward, the others pointing backward.  It wore a pair of shorts in some kind of skin-tight material.  (Author’s note: For those of you who’ve played Final Fantasy VII, just imagine the Summon Materia Bahamut plus the arm blades, color difference, and shorts.)

            “A dragon!” Shinji exclaimed.

            “Ah, so.” The creature stated in perfect Japanese. “I’m on Terra.  Good to be back.”

            “Who are you and whose side are you on?” Shinji asked.

            “That depends.”

            “On what?” Rei inquired.

            “We’ll see,” the creature cryptically replied before leaping into the air and flying off.

            “Damn!” Shinji swore. “Well, I guess it’s back to base for now.”

 

NERV HQ, debriefing room

 

            “What do you mean, you didn’t find anything out about it?!” Gendo screamed.

            “Shinji asked it who it was and whose side it was on,” Rei answered.

            “Then it flew off,” Shinji added, “saying ‘we’ll see.’”

            Before Gendo could respond, the trio heard knocking.  Gendo walked over and opened the door to see a young man standing there.  He stood six feet tall, with black, shoulder length hair, wearing a black shirt, black jeans, black sneakers, black single-lens wraparound shades, and a black leather trench coat

            “What do you want?” Gendo snapped.

            “Are you Commander Ikari?” the young man asked.

            “Yes.”

            “Ah, good.  I’ve been looking for you for the past few hours.  You’re a hard person to locate.”

            “I’ll say it again.  What do you want?  I’m busy right now.”

            “Oh, yes.  Forgive me.” The young man said as he bowed. “My name is Raiu Kusanagi.  I was told to find you.  I’m an engineer.”

            “We could use another engineer.  How old are you?”

            “Sixteen.”

            “You look like you’re at least twenty,” Shinji stated bluntly.

            “Appearances can be deceiving,” Raiu responded cryptically.

            I’ve heard that voice somewhere before, Rei thought to herself, it’s so familiar.

            “How skilled are you?” Gendou inquired.

            “That depends.”

            Now I know I’ve heard that voice before, Rei thought.

            “On what?”

            “Which EVA you want me to work on.  I can repair and maintain any EVA, depending on which one it is.”

            “Alright then.” Gendo stated. “If you’re so sure of yourself, follow me.”

 

EVA Docking Bay

 

            “We’ve been having constant problems with that EVA.” Gendo stated, pointing to EVA-00. “Find it and fix it.”

            “I can tell you right now what the problem is.” Raiu replied flatly. “External power source.”

            “What other kind of power source is there for an EVA?” Shinji asked. “The S2 engines won’t work with EVA-00 and EVA-02.”

            “Not a problem.  Just give me the design specs of an S2 engine, and I’ll build ones for each of the EVAs.”

            “First, find the problem I was talking about and fix it,” Gendo ordered, inwardly smiling since there was no problem.

            “Alright.” Raiu stated as he jumped over the railing before anybody could stop him.

            They ran up to the railing and looked down to see Raiu rapidly climbing down the cross beams holding up the catwalk.  In a matter of seconds, Raiu was on the ground, walking toward EVA-00.  He reached the giant robot’s foot and studied the EVA.

            “Aw, bloody hell, this is gonna be fun!” Raiu shouted to everyone.

            Having said that, Raiu began indiscriminately ripping the armor off the EVA and tossing pieces aside.  He circled the foot, still ripping out parts.  Raiu then climbed the leg, ripping more parts of the armor away.  Once he had made it up to the thigh, he jumped down.  Everyone looked away, expecting him to go splat.  When they heard no sound, the looked back to see Raiu spraying the leg of the EVA in some sort of clear substance.

            “Just what is he doing in there?!” Gendo shouted to an engineer that happened to be standing close to EVA-00 after staring at the EVA for almost half an hour in shock.

            “I don’t know!”

            As Gendo, Shinji, and Rei began walking toward the elevator, the EVA’s leg began glowing bright blue.  The glow soon disappeared, leaving what appeared to be the old armor of the leg in place.  Raiu climbed partway down the leg and then jumped off, landing safely on his feet in a crouch.  He stood up and tried to wipe some of the substance from his face, but only succeeded in smearing it more.  Raiu finally got a hold of a rag and was wiping himself off when Gendo and the two teens reached him.  Gendou grabbed the teen’s shirt and pulled him close to his face.

            “Do you realize that you have just ruined over two decades of work?!”

            Raiu just stared at him blankly.

            “Y-you accomplished that much after two decades?”

            “Yes!” the Commander snapped. “And you just ruined it!  You’re fired!”

            “I haven’t even been officially hired yet!  In half an hour, I fixed two decades of screw-ups.  Just ask your computer techs up in the control room to scan the leg.  The gel enhances an EVA beyond what you think is possible.”

            As if she’d heard Raiu, Maya contacted Gendo over the intercom.

            “Before you do anything rash, Commander, I think you should hear what we found out.  After Raiu finished with EVA-00’s leg, the power drain dropped to less then a fraction, strength and endurance was doubled, and efficiency is off the scale.  Not to mention the fact that the armor is now three times stronger.”

            “How long will it take you to do this to all the EVAs?” Gendo asked.

            “Not only can I do that, I can redesign the Entry Plugs so that it takes a mere thirty seconds to activate an EVA and synchronize it with the pilot.  Plus synchronization will be a hell of a lot easier.”

            “Holy shit!” Shinji exclaimed.

            “The only problem is that the Entry Plug will have to be placed in the EVA’s brain case instead of the spine.”

 

Several days later, midnight

 

            Gendo sat at his desk, pondering the arrival of Raiu.  The young man had proven to be a valuable asset, however strange he may be.  Gendo had almost denied Raiu permission to redesign the Entry Plugs, then realized the merits of almost instantly activating all three EVAs with increased power and armor at no cost to Tokyo 3.

            “I’ll have to keep my eye on that boy.” Gendo thought aloud. “He may just prove to be more trouble than he’s worth.  At least I uploaded the security protocols yesterday.  If he proves to be a detriment, he won’t be able to get into the programming.”

            Elsewhere, Rei lay in bed, – still in her Plug suit – unable to sleep after her and Shinji having decided to stay the night at NERV after a late night harmonics test.  She and Shinji had agreed that Raiu’s voice was strangely familiar.  They just couldn’t place where they’d heard it before.  She remembered Gendo’s face when Raiu started ripping the armor off EVA-00.  The thought brought a rare smile to her face.

            She stood up and walked to her door.  Rei opened the door and crept down the hallway, not wanting to be caught.  When she saw that nobody was patrolling the halls, she relaxed into her normal walk.  Lost in thought, Rei wandered the halls.  She stopped when she heard noises coming from the other side of a door.  She looked around and realized she was just outside the EVA Docking Bay.  She opened the door and walked into the control room.

            “Hello.  Didn’t expect you of all people to be here.”

            Rei looked up and saw Raiu working at a console.

            “How’d you know it was me?  You weren’t even looking at me.”

            “You just gave yourself away, Rei.  I wasn’t really sure who it was.  I have yet to learn each of your individual footstep patterns.  It’s a little habit I have.  Haven’t grown out of it.”

            “What are you doing here?” she asked.

            “Running a test.”

            “On?”

            “A new weapons array I installed in the EVAs.  The only problem is that the programming won’t accept the combination of robotic and organic parts well enough to get it to work.”

            Rei walked up and looked at the schematics Raiu had been working on.

            “You said you were an expert,” she whispered.

            “That’s a bit of an exaggeration.” Raiu laughed. “I just said I’m good at it.”

            “And fast.”

            “Yeah.  Guess I proved that by upgrading three EVAs in less than a day, eh?  You think you can do anything with this stupid program?”

            Raiu watched with interest as Rei typed in a series of commands.  His jaw dropped and his eyes bugged out as the computer flashed a phrase across the screen.

            “Configuration acceptable,” the computer’s audio systems droned.

            “How – wha da – but I – ARGH!!”

            Rei suddenly burst out laughing.  Raiu glared at her.

            “What’s so funny?!” Raiu snapped defensively.

            “The look on your face!” Rei gasped between laughs. “It was priceless!”

            “Hey!” Raiu exclaimed in realization.

            “ . . .?”

            “That’s the first time you’ve shown happiness – hell, any emotion - since I got here.” Raiu replied. “And you laughed.”

            “Oh.” Rei replied as she finally stopped laughing.

            On the other hand, she was still smiling slightly.  She quickly hardened her expression and looked away slightly.

            “What’s wrong?”

            “Nothing.”

            Raiu cocked an eyebrow but let it slide.

            “Anyway, what did you type in?”

            “An override command.  Commander Ikari set up the computer to lock out any changes that tried to be made to the EVAs and the programs associated with them.”

            “Why’d he do that?”

            “I really don’t know.  I mean, he’s the Commander of NERV, so nothing major happens without his consent.”

            “Hmm, weird.  He’s probably just a control freak.”

            Rei’s hand snapped up from her side to slap Raiu when something stopped her hand.  She looked down to see Raiu gripping her wrist.  What surprised her most was that her hand hadn’t even gotten three inches away from her side before he’d caught it.

            “How –”

            “Why?” Raiu cut her off, ignoring the surprised look on her face.

            “ . . .?”

            “Why did you try to slap me?” he asked in a soft voice.

            “You insulted Ikari.”

            “You care for him.”

            It was more of a statement than a question.

            “Yes.  He is like a father to me.  He also created me.”

            Raiu quirked an eyebrow at this.

            “What are you talking about?”

            Rei briefly related her past.  Raiu shook his head.

            “I owe him at least my loyalty since he created me.”

            Raiu sighed as he stood up, let go of Rei’s hand, took his trench coat off, and entered a series of commands.  Before Rei could say anything, Raiu had gotten into the elevator and the doors were closing.  Rei ran in and stood next to Raiu.

            “Just what are you doing?”

            “You’ll see.”

            The elevator doors opened, revealing the Docking Bay.  Without saying a word, Raiu walked over to an Entry Plug and opened it up.

            “Get in.”

            “Alright,” Rei replied, suddenly nervous as she sat down in the Plug and closed it.

            Raiu pushed a button and the Plug slid into EVA-00.  He walked over to another Entry Plug as EVA-00 came to life.  He pressed a button on a small pad and got into the Plug.  The Plug automatically slid into EVA-01.  The EVA came to life and turned toward EVA-00.

            “Ready?”

            “Raiu?!” Rei exclaimed in shock. “You’re piloting EVA-01?”

            “Yeah.  I installed a temporary programming block.” Raiu lied. “The EVA thinks I’m Shinji.  So, you ready to test these babies out?”

            “Alright.”

            The lift carried the two EVAs up to the surface.  Once there, Raiu activated the jets on EVA-01’s back.  He turned back to EVA-00 and waited for a few moments.

            “You have jets too, y’know.”

            “Oh.”

            Rei activated her jets and hovered next to Raiu

            “Catch me if you can!” Raiu taunted before zooming away.

            Rei shot after him, easily catching up to him.

            “Is that the best you can do?!” Rei asked over the comm., a rare rush of excitement filling her.

            Raiu let out a cackling laugh and set his jets to full power, leaving Rei behind in less than a second.  She gave chase and froze in shock when she saw Raiu fighting an Angel.

 

NERV HQ

 

            The screeching of alarms woke half the base in less than a minute.  Shinji ran to the EVA control room.  He was about to head for the Docking Bay when Misato stopped him.

            “Shinji!  What are you doing here?”

            “I heard the alarm and came running.”

            “Well, if you’re here, then, who’s piloting your EVA?”

            “What?”

            Shinji ran over to the window and saw both his and Rei’s EVAs were missing.  Before anybody could say anything, EVA-01 landed heavily on top of the lift, leaving dents where its feet hit.  A large scorch mark adorned its chest.  It then walked over to its dock as EVA-00 landed, albeit gentler than the first EVA, and entered its own dock.  A similar mark was imprinted in EVA-00’s armor  The Entry Plugs ejected and opened.  Rei was the first to step out, followed shortly by the other pilot, whose face was covered in sopping wet hair.

            “Hell yeah!!” the pilot yelled, easily letting everyone know who it was. “Now that was fun!!”

            “Raiu!!” Gendo roared as he and Shinji exited the elevator. “You are in deep shit!”

            Raiu pulled his hair back and walked up to Gendo.

            “What?  Not gonna thank me for destroying an Angel with the new weaponry I designed?”

            “You piloted an EVA that doesn’t belong to you.  And you used new technology that I hadn’t approved of yet.  You had no right to do so.”

            “No right to test out the new weaponry before letting Shinji use it and risk having it blow up due to a malfunction?  You’re full of it.”

            “Wait a second.” Shinji interrupted before his father could say anything. “You said you destroyed an Angel.  I thought they were all gone.”

            “Guess not.  Bastard got the drop on me.  Pretty powerful too.  Almost blew a hole through EVA-01’s shielding.”

            “Rei!” Gendo called out. “What do you recall about this ‘Angel’ Raiu supposedly killed?”

            “All I remember is that I caught up to him after chasing him for several minutes,” the girl called back, delayed by technicians, “only to see him fighting an Angel.  Then nothing until we were back at the launch tube.”

            Just then, Maya came running up to Gendo.

            “Uh, sir.  You might want to take a look at this read out.”

            Gendo reluctantly read the report and snapped his head up toward Raiu.  He turned back to Maya and whispered into her ear.  She nodded her head and went back up to the control room as Gendo turned back to Raiu.

            “How do you explain this?  Forget that, how were you even able to pilot EVA-01 in the first place?”

            Raiu grabbed the report from Gendo’s hands and looked it over.

            “Explain what?”

            “The Sincro rate.  The closest percent to that has only been achieved twice.  Both times, the pilot was absorbed into EVA-01.  Somehow, though, Shinji managed to rematerialize.”

            Rei walked up behind Raiu and read the report over his shoulder.  When she saw the Sincro rate, she stared at it in shock.  Raiu stepped away from Rei and snapped his fingers a couple of times, snapping her out of her shock.  He then turned back to Gendo and looked at the report again.

            “1000%?” Raiu asked, puzzled. “I thought I was better at EVA synchronizing than that.  All right, I can tell you what I know.  But, only if it stays between the four of us for now.  Alright?”

            Gendo thought it over for a few moments before replying.

            “Alright.  Let’s go to the debriefing room.”

            When they got there, Raiu turned to the group.

            “Whenever I pilot an EVA, my body shuts down and I basically become the EVA.  Even EVAs designed to function for only a certain pilot.”

            “How is that possible?” Shinji asked. “Only Kaoru was able to -”

            Shinji’s face shifted from confused to shocked as he came to a realization.

            “Rest assured.  I’m no more Angel than any of you three are.  Aside from that, I’d rather not explain,” Raiu replied.

            “We’re not leaving until you do,” Gendo stated firmly.

            “Fine.”

            Raiu lowered his head and removed his shades.  When he looked up at the other four again, it was through silver cat eyes.  Seeing the surprise on their faces, he explained.

            “I wasn’t born.  I was bred in a test tube along with one other.  We were designed to be the perfect pilots for EVA Units.  But, the head of the project was extremely corrupt.  He wanted to brainwash us, make us mindless drones, following commands without question.  I overheard him one day, talking to someone about selling us to the highest bidder as the perfect war machine, provided the buyer had EVA Units.  Upon hearing that, I decided to escape.  I told my brother, and he agreed to leave with me.  As we were escaping, though, he was captured.  He managed to break free, but they didn’t want to risk anything.”

            Raiu looked around with pain filled eyes.

            “They killed him.  Four bullets.  One to the heart, one to each lung, and a final one to the head.  With his dying breath, my brother said one last word to me.  He said, ‘live.’  I ran until I could run no more.  I learned what I could about the world outside the complex while evading the teams they sent out after me.  I soon heard about NERV and came to Japan, hoping to find sanctuary from my hunters.  All I ask in return for enhancing your EVAs is a place to stay, a steady paycheck, even if it’s only minimum wage, and protection from them if they ever find me.”