SHINJI X
by Gunman

Disclaimer: I do not own Shinji, the EVA universe, or any other anime with people possessing super human powers.

Author's Notes: This one has been on my computer for a while now. And as I've been working on a dozen other projects, not to mention working in general, I just recently managed to find the time and the will to finish this story. At least to the point of a first chapter.

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Chapter 1
The New Weapon X

"SHINJI! DON'T YOU DO ANYTHING STUPID!" Misato Katsuragi shouted through the comm. link to Unit 01 as the boy pilot continued to battle the Angel.

Inside the Geofront the Third Child of NERV was focused on a single task... saving his friend and potential love interest: Rei Ayanami.

Asuka was still in a coma following her brain-scrambling by the 15th Angel. Shinji had been delayed in trying to help his friend, who had been sent out to fight the Angel, by his father for an unknown reason. However, Shinji's sense of urgency had pushed Unit 01s synch ratio to a super high level just like during the 14th Angel attack.

Everyone remembered what had happened last time.

"EVA HAS GONE BERSERK!" Maya Ibuki shouted.

The strange glowing, snake-like Angel had tried to initiate first-level contact with Rei and her Unit 00, which was what Gendo wanted. It was all part of his plan. But his plan now had one terrible flaw in it... Shinji.

Somehow his synch rate with Unit 01 had caused him to override all commands that Gendo had tried to initiate.

The Dummy Plug System... the shut down of Unit 01... even the pressurization of the LCL inside the entry plug... all failed. It was as if Unit 01 itself was preventing NERV from trying to regain control of the biomechanical weapon.

It might have been better though, as the Angel was currently trying to painfully merge with Unit 01 after Shinji had taken the Angel out of Rei's unit. However, the pain that Shinji was feeling now was a direct result of that action.

An action that had only one recourse.

"UNIT 01 HAS INITIATED SELF-DESTRUCT MODE!" Maya screamed as she desperately tried to override the command.

"WHAT? How The Hell Did He Know Where The Damn Button Was?" Misato shouted then barking orders to Makoto and Shigeru to help Maya.

"You're Surprised?" Ritsuko shouted, trying to help her assistant, Maya, shut down the Eva. "He's Been Depressed For Weeks!"

"That Doesn't Mean..."

"COUNTDOWN INITIATED AT THIRTY SECONDS!" Shigeru shouted.

Everyone watched, helplessly, as the timer counted down.

(Rei...) the crew heard Shinji's voice through the intercom. (I'm sorry I couldn't do better than this. I love you.)

Everyone could have sworn they heard the albino girl gasp inside her Eva.

"TWENTY SECONDS!" Shigeru shouted.

(Misato... thank you... for trying your best to take care of me... like a mother...)

Tears filled the purple-haired Major's face as the countdown continued. Shinji... she thought.

10, 9, 8, 7, 6, 5, 4, 3, 2, 1...

No other words were spoken, as the timer reached 0.

The blinding flash lite up the Geofront, contained within the unusually powerful AT-Field that the boy threw up around him to protect everyone he could from the blast. The fierce rumbling shook the NERV crew off their feet, their eyes covered as Unit 01 vanished.

From the bridge the reactions were mixed.

Gendo was upset. Misato and Maya were crying. Ritsuko's lip quivered. And Rei... felt tears emerge from her eyes.

I am... crying. Rei thought as she wiped away the moisture from her cheek. Her injuries from the Angel attack had caused her Entry Plug to eject, and Rei was watching from outside her Eva. Before now she had never known what it was to lose something. Guilt, shame, and now... love, for she had effectively lost the only who actually cared for her. Shinji... my Shinji...-kun. She thought as she dropped to her knees as tears flowed down her face.

Misato was the first person to notice this... and tried to connect to the Eva.

"Rei..." she whispered, "Are you... alright?"

(Major?) she whispered into the mic. (Shinji... he is... is...)

"I know, Rei. I know." she said, wanting to embrace and hug the girl, thinking that she herself needed it just as much, and that Rei had called Shinji by his first name. Not something that she would have noticed at first.

Gendo was fuming a bit at what he considered a disgustingly touching scene.

"What is the status of the Angel?" he asked, breaking the sad tension.

"Blue... blue pattern has gone silent. Pilot Ikari has... destroyed it." Maya choked back the tears.

"What about Unit 01?" he asked.

"All the readouts are negative. Magi reports that... Unit 01 has suffered... 98-percent damage." Shigeru stated in confusion. "It's like it's... virtually all gone."

Gendo growled at that.

"What about the core and Entry Plug?" Ritsuko asked.

"Uh... sensors are reading a faint power signal coming from Unit 01's S2 Engine... there's also some residual energy coming from the remains of the Entry Plug." Shigeru said.

"But.. shouldn't the plug have been ejected before it exploded?" Misato asked.

"No. All ejection controls were overridden... by Unit 01." Ritsuko explained.

The purple haired woman and the blue haired girl just cried as they heard this.

Gendo was getting upset at the weakness everyone around him possessed.

"Ritsuko." the dark man spoke.

"Sir?" the blond woman replied.

"Have the remains of Unit 01 taken back to the cages... we'll see what can be salvaged and put into the remains of Unit 03." he ordered.

"Yes, sir." Ritsuko exclaimed with some distaste.

"And we'll need to see about finding a replacement pilot, as all our pilots are now... useless." he said with conviction.

Shinji dead... Asuka in a coma... Rei an emotional wreck. Ritsuko thought. Though part of her was actually enjoying seeing the little doll in pain, it hurt that the source of the pain was Shinji.

Ritsuko had nothing against the boy. In fact she considered him a better person than his father.

Gendo dismissed everyone and went to his office.

Once Rei had gotten herself back to base, cleaned up and dressed in her school uniform (her only outfit really), she was met outside the locker room by Misato.

"Rei..." the purple-haired woman said.

"Major..." the bluenette girl replied.

Misato pulled Rei into a tight hug as she cried. And oddly enough... Rei didn't pull away from the woman whom she had never shaken hands with before, and was now being hugged by her.

"Come on Rei. Let's get you home." Misato said to the girl, turning away and leading Rei to the garage.

She gasped when she felt Rei's hand clutch her own. If Misato didn't know any better, she could have sworn that the girl didn't want to be alone now.

In a way... she didn't want to either. But before she could ask...

"Major?"

"Yes, Rei?"

"May I ask a favor of you?"

Under the circumstances, Misato couldn't say 'no'.

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In the large dark office of Gendo Ikari, the scheming commander and collaborating doctor were talking.

"I want Plan X up as soon as you retrieve the boy from what's left of the entry plug." he said as he sat at his desk, hands folded in front of his face.

"Plan X?" she gasped. "Are you sure?"

"You have the information concerning it, don't you?"

"Of course." she said, stuttering slightly. "But... who will you use?"

She only asked because it didn't seem as if he wanted to use Shinji, since he was dead anyway.

"What's left of the Third Child." Gendo stated.

Ritsuko gasped. "Shinji's alive?"

"Barely. I want you to get started immediately."

"But... he's your son." she said, suddenly wondering why she was trying to appeal to his humanity.

Or lack thereof.

"My son is dead. Begin Plan X as soon as you can." he said without emotion.

"Yes, sir." she said and walked out, not letting the man see her scowl of disgust.

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Misato and Rei arrived at Misato's apartment, the former warmth that had once filled the dwelling obviously gone.

Misato had invited the quiet and lonely girl to her apartment, mostly because she felt she too had suffered a terrible loss like she had.

Misato had offered Rei something to eat, but was politely declined. Misato herself didn't feel like eating anything either. Her own 'cooking' felt more like an inconvenience, so she decided to drown her misery in her beer. She had lost the two most important people in her life now. The first had been Kaji, the man she had loved, and the second was Shinji, the son she always wanted.

And so she drank.

Rei on the other hand found Shinji's room, not really being in a talkative mood with the Major.

The second she stepped through the door to his room she noticed that, like Unit 01, it smelled like him. Like Shinji.

She walked over to the bed and laid down, immersing herself in the scent that was Shinji. She then noticed his SDAT sitting next to the pillow. A tear welled up inside her as she put the plugs into her ear and pressed the Play button.

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(NERV Infirmary)

Shinji's body was wheeled into the dark room, all manner of high-tech electronic device that could be conceived was around them.

Ritsuko dismissed the orderlies with a wave and leaned over the body of the Third Child.

She looked at him, running a hand through what was left of his mussed and frayed hair. His skin was burnt and cut up, his plugsuit looking like it was nearly fused to his body. His nerve endings were most likely dead and if his breathing were any more shallow, he'd have been declared dead.

Officially he was, but that mattered little to Gendo.

Fucking bastard! He's your son! Ritsuko said, fighting back tears. There were no cameras in this room, but she managed to keep her composure up well. Well... if he wants Plan X, he'll get Plan X! she thought as she leaned down and kissed Shinji's burnt forehead. Yui, I've never had any love for you, and I have nothing but loathing for your husband. But your son... him, I'll save!

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Ritsuko worked long into the night preparing the boy for the final implementations of Plan X. She had been able to use special adrenaline and booster shots to accelerate his bodies natural healing ability but also numb the pain he was under. She also had to cut off the remains of the plugsuit that was either burnt or melted off his body. A lot of the process involved making sure that there were no more foreign objects on Shinji's body as well as cleaning the wounds and such.

It was nearly three in the morning when Gendo and his hand-picked staff arrived.

"Is he ready?" Gendo asked.

"Yes, sir." a tired looking Ritsuko said. "We can safely move him to the experimentation room."

"Excellent." the grim man said and silently motioned for the orderlies to move Shinji out. He turned back to the woman. "Are you coming, doctor?"

"I've been up all night. I need coffee." Ritsuko huffed.

"Very well. Ten minutes." Gendo said and then left.

Ritsuko shot daggers at the back of his head, wishing she had real ones.

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"You are five minutes late, doctor." the unhappy Gendo said as Ritsuko walked in.

"Blame the coffee machine, sir, not me." Ritsuko complained as she went right to work.

The other techs and lab workers busied themselves with the preparations and special equipment while Gendo conferred with Ritsuko.

"So, is this plan sound?" he asked the woman.

"Yes. However, the project has never had any real success." Ritsuko explained.

"What do you mean?"

"The last known success was a man named James Howlett, back in 1955. Unfortunately another casualty of Second Impact." she continued to explain as she calibrated the special equipment that she needed for the experiment. "As you know, the Weapon X Project was originally designed by the Canadian government to create artificially enhanced super soldiers to protect their country from a variety of threats. But the project was discontinued when one of their test subjects, one Victor Creed, went crazy and killed virtually everyone in the lab. James Howlett was the only known success, but he escaped in the chaos."

"And what about Creed?"

"His enhancement eventually resulted in his death. His body couldn't handle the tremendous strain it had been put under. While it gave him incredible strength and power, it overloaded his body to the point of extreme exhaustion."

"Extreme exhaustion?"

"Yes. He burned out. Almost literally. According to the last autopsy reports all his internal organs were pushed beyond their intended capacity and limits, unable to be healed, they were liquified."

There's a nice image. he mentally huffed.

"Anyway, the scientists at the time speculate that James Howlett survived because of an anomaly in his physiology." Ritsuko continued.

"You're referring to his healing factor."

"Yes. A genetic mutation that was almost biblical in status."

"The reports on the project vaguely mention it."

Really? It was only the key to the project's success. "That's what the reports indicated." she said.

"Interesting."

Then a thought struck him.

"And you suspect that the Third will not survive the process without one."

She fumed at his use of the term 'Third' as it applied to Shinji. "Yes. It would be a waste not to get this right the first time." she said.

"Trial and error are all parts of the scientific process." he said dismissively.

Of course you would say that about your own son. She mumbled angrily. "We don't have any other subjects, sir. And there are also time constraints to consider."

"Time, yes. We have more than you think."

"In that case..." she said then turned back to the other techs. "Listen up, people!"

The technicians gave her their full attention.

"We're going to go slowly with this, try and get it right the first time! Estimated time two-hours per stage of experiment."

"Two Hours?" Gendo gasped. "There are SIX stages to the process!"

"Yes. And I want to get each one right." Ritsuko stated.

Gendo huffed. "Very well. Notify me when the final stage is getting ready to be implemented."

"Yes, sir." she replied.

With that, Gendo left.

Ritsuko grinned internally as he left. Now, let's do this.

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Shinji was carefully laid upon the table as the technicians gathered around him.

"Start level, Dr. Akagi?" one of the techs asked.

"Genetic mapping, level seven." she said.

"Full body then."

"That's right."

"Understood."

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Ten hours later...

The first stage of the process involved a complete genetic mapping of Shinji's body, which also included past data taken of him, involving every type of scanner and recording device they had. Every cell had to be accounted for.

The second stage of the process involved fine-tuning and locating the necessary entry points of Shinji's body for the special medical needles to be inserted. Points that had to be programmed into the computer and the mechanical needle arms, and be accurate to within a couple millimeters.

The third stage of the process involved repairing the damage to Shinji's body, first with the physical healing of cloned skin made from Shinji's DNA. A process done at the same time as the computer programming for the insertion needles.

The fourth stage of the process involved genetically altering the specific DNA strands that would give Shinji an enhanced body, specifically his bones and muscles.

The fifth stage of the process involved genetically altering the rest of Shinji's body. This included his eyesight, auditory systems, physical strength and regeneration powers.

It had been an exhausting process to prepare Shinji for the final stage of the experiment, mostly spent mapping, cleaning, repairing, and enhancing him.

Actually enhancing all of Shinji's body, not just his healing ability.

"All right, test time." Ritsuko said as she picked up a scalpel and stepped up to the boy. "Nobody breath." she said as she made a long incision into Shinji's left arm.

Everyone just stared at the boy as the long deep cut quickly vanished, the wound healing itself up, starting from where Ritsuko started to where she finished. There was nothing to indicate that there had ever been an incision. No scar, no line, nothing.

Ritsuko breathed a sigh of relief. Bet you could have used this when you first piloted, Shinji-kun. She thought. "All right. Artificially-enhanced healing factor functioning better than expected. We can begin the final process." she said as the techs lifted Shinji off the table and carried him over to the large glass and metal case in the center of the room.

They set him onto the metal stretcher that was suspended above it and attached a breathing apparatus to his face before lowering him into the strange liquid.

"We're ready to begin, Dr Akagi." the tech said.

"All right. Submerge Shinji into the tank." Ritsuko said.

No one noticed, or cared, that she used Shinji's name.

Just then, Gendo walked into the lab as Shinji was fully submerged into the tank.

"Akagi. How is the project coming?" Gendo said.

Damn it! Who summoned him? "We're in the final stage of the process." she said, miffed that he was here.

"And the test subject?"

She glared at the man with contempt, for referring to Shinji as a 'test subject'. "Responding well."

"Then let's get this project underway."

Ritsuko nodded, knowing that her modification to the process would go unnoticed.

The original intent of the Weapon X project was to graft adamantium metal to the skeletons of a select group of individuals in order to turn them into superhuman agents. A secret strike force that no one else had.

And naturally, the stronger the bones of these agents, the stronger their physical strength and even their skin.

At least, that was their intention.

The secret to this project: Adamantium, a virtually unbreakable metal alloy artificially created by unknown scientists. Whether or not they were total geniuses or complete wacko's was never known. But the metal they created was a success. The problem was that the adamantium had to be kept at super heated temperatures in order to make it malleable and shaped into whatever they wanted. Once it cooled, however, the metal itself becomes totally unbreakable and impossible to chip, bend, break, rust or even super-heat to reforge.

However, only one person ever survived the bonding process, and that was because of his unusual and natural healing powers. All other attempts to graft the adamantium metal to other select individuals had met with horrible failures and even more horrible deaths.

To compensate, and thus save Shinji's life, Ritsuko had augmented the boy's physiology, giving him an artificially enhanced healing factor. It was hoped that this would be the key to saving his life as the process was initiated.

And if completely successful, Plan X would give them a new super weapon who would be of more use to them than Shinji had been as a pilot. Shinji's Eva was gone, so there was little point to keep Shinji around, until Gendo suggested Plan X to get some use out of the boy.

"How is the process going?" Gendo asked as the mechanical arms moved into place above Shinji.

"As well as can be expected, considering this is our FIRST test subject." Ritsuko groaned, with emphasis on 'First'.

The pair watched as Shinji was still asleep under the water, the mechanized syringes locking onto the exact entry points on his body.

"Are the straps and cuffs secure?" Ritsuko asked one of the techs.

"Yes, doctor." the tech replied.

"Those straps and cuffs are leather and titanium. They'll be the only things keeping him contained, and us safe, when the final process is initiated." she explained.

"Is it that bad?" Gendo asked.

"Unfortunately, yes. Even though Shinji's half-dead, his nerves numbed and he's teetering on death, this process is going to be extremely painful. If there's any life in him, he's going to wake up with an urgent need to scream. He'll thrash around and hopefully be unable to break free."

"You overestimate the Third Child, doctor. Even fully conscious and unhurt he would never be able to break out of plastic paper straps."

Ritsuko glared at the man, seeing him laugh at his own bad joke.

Just wait, Gendo. If I'm right about this...

The mechanical syringes whirred to life as they moved towards the unconscious Shinji.

Ritsuko winced as the needles were inserted into his feet, his ankles, his thighs, his hips, his spine, his rib cage, his upper arms, his lower arms, his hands, the back of his neck, and his skull.

She had seen experiments where needles were inserted into the bone and a chemical was injected. And granted that the subject was always unconscious and drugged up, but this magnitude of use was beyond anything she had ever seen. The pain of drilling into Shinji's body was enough, but the heat from the liquid metal Adamantium would have caused anyone to scream in absolute and indescribable pain.

She felt truly sorry for Shinji, and what was to happen.

Suddenly, Shinji's body jumped.

"What's happening?" Ritsuko asked.

"Adamantium bonding process is taking effect!" a technician shouted.

"Life signs weak, but stable!" another tech shouted.

"Sensors indicate adamantium process has spread to entire skeletal structure." a third tech shouted.

Shinji thrashed briefly.

"Doctor! Heart rate has just jumped!" The first tech said.

"Nervous system is firing on all levels!" The second tech said.

"Pain threshold has reached it's limits!" The third tech said.

Ritsuko looked over to Shinji in the tank, her eyes frozen as she watched him thrash violently and continuously. It looked like he was screaming.

"Activate sedatives! Double Dosage!" she ordered.

The order was carried out and the drugs were pumped through the tubes into the boy.

"No Response!" a tech shouted.

"What?" Ritsuko gasped.

"The sedatives aren't working!" a second tech shouted.

His healing powers are negating them. Just like I thought. Ritsuko mused.

Suddenly, Shinji exploded from the tank, the titanium cuffs and leather straps breaking like wet paper.

"Security, get in here!" Gendo ordered.

A half-dozen men in black suits stormed the room, their guns drawn.

The wires and tubes were still hanging off of Shinji as he glared angrily around the room.

"Secure him!" Gendo shouted.

The guards and the techs rushed the boy, the techs armed with emergency tazers, the guards with their guns.

Shinji's world became nothing but red, pain lanced his arms as without warning, six claws shot out from between his knuckles, three on each hand and each a foot long, his arms instinctively lashing out and impaling one of the techs and one of the guards.

Everyone in the room froze as Shinji let loose a ferocious scream and quickly shot through the air. The guards opened fire, but because Shinji was leaner and smaller than they were, hitting him was next to impossible.

His claws cut into numerous people, a count that Shinji couldn't keep if he even cared to. Screams and blood filled the room.

Shinji then saw two people standing in his path.

One a blond haired woman in a white lab coat. One a man with a brown beard and tinted glasses. He thought that they looked familiar.

The bearded man pushed the blond woman in front of him, towards Shinji himself.

Bastard! Ritsuko thought as she fell towards Shinji.

However, Shinji lunged forward, leaping over Ritsuko and heading straight for Gendo. The grim man turned as the boy screamed heavily, a heavy downward slash taking a chunk out of Gendo's face before he knew what happened.

The man fell to the ground as Shinji saw his way out, and took it.

Ritsuko quickly moved to Gendo, but kept her eyes on the door where Shinji had escaped.

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In another part of the world, a young girl woke up with a start. A throbbing in her head caused her to shout, unleashing a torrent of psychic force that blasted half of her furniture out of her room.

In seconds, a half-dozen other people exploded into the room. They were lead by a large man with skin that seemed to be made of steel.

"Iris? What's wrong?" Eric, the large man of steel asked.

"I'm not sure. I felt...pain." the young girl said.

"Yours?" Nancy asked, the purple-haired woman appearing by her bed.

"No. Someone else." she stopped holding her head and got up to get dressed. A fierce determined look in her eyes now. "Get the jet ready. All of you get packed. I'm sure I'm going to need your help."

"The jet?" the blond-haired Ginji asked

"Our help?" the red-haired Robin asked.

"What for?" the blue-haired Toga asked.

"And where are we going?" the blond-haired Naruto asked.

"To Japan. I'll know more when we get there." Iris said as she shimmied out of her nightgown.

"Okay. But do you want to tell us why?" Robin asked, the boys looking away from the girl.

"I sense a person in pain. Someone in Japan has been exposed to some form of genetic alteration. Experimented on. We have to find him and help him." Iris said.

"Wait, wait, wait. You felt this guy, all the way in Japan?" Naruto asked.

"Yes. I did."

The group looked at each other in shock. She turned to face them.

"Keep in mind that I found all of you the same way." she said.

The group relented.

"But why us?" Nancy asked.

"Because we are the only ones who can." she said.

"How do you know this?" Robin asked.

"I felt it. I've never felt pain or anger like this before. If we don't hurry, the situation could become serious. Deadly serious." she said as she grabbed her teddy bear.

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Authors' Notes:

Hope everyone enjoyed this little first chapter of 'Shinji X'.

This is a story I've been working on for some time, but never thought it was good enough to post. Chapter One is finished, and most of Chapter Two is done. Chapter Three I think will introduce Shinji and the others to this mysterious group of individuals who are coming to help Shinji.

I'll leave it to you to figure out who is who and what powers they have.

No hints.

Also, if you want you can think of this as an X-Men crossover, though I won't be using the X-Men themselves for this.

Plus, I am also giving you this story now to tide you over while I finish up my other stories.

See you later and give me lots of reviews.