Disclaimer: Neon Genesis Evangelion is copyright by A.D. Vision and was created by Studio Gainax animation. All their characters are used without permission. Plus there's another disclaimer I'll have to place in other chapters if I decide to continue this.

Contrary to my normal style of writing, there will be no massive writer's commentary at the beginning of this fic, just a simple explanation. The reason I did this was to put a new spin on an old (but very cool) idea that has been used countless times. While some Shinji-with- a-spine fanfics are very cool, most are just repeats of the same story. My goal with this fic is to do a cool badass Shinji story that has never been done before. So sit back and enjoy another WDCain masterpiece.

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Shinji, Lord of the Sith

Part One:

A New Beginning

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The Year 2015 AD...

"Damnit! Why did I have to lose him at a time like this? growled Misato Katsuragi as the drove through the evacuated streets of Tokyo 3. She shook her head in frustration as she looked at the picture of the young child she was to find. The name Shinji Ikari was printed at the bottom of a photo of a pathetic looking kid in a school uniform with shaggy dark hair. "Lord Almighty, just where is this kid?" she asked to no one in particular.

"Man... just where is she?" muttered Shinji Ikari to no one but himself as he walked around the empty streets of Tokyo 3 as he stared at a photograph of a beautiful purple-haired woman who was bent over suggestively along with an arrow pointing at her cleavage saying 'Get a load of this!'

In his other hand was a bag of some clothes to get him by along with his trusty SDAT Player. He frowned as he pulled out a letter from the bag. It was address from his father and had only one word written: COME.

Shinji shuddered and quaked at the thought of meeting him again. Best to get this over with, I want to head home soon.

Shinji reached for a payphone, hoping to connect Misato's cell phone. "We're sorry, all lines have been disconnected," came the voice machine at the phone company. Shinji sighed. Could this day possibly get any worst?

That was when he saw the forth Angel and started screaming like a little girl. Fortunately, that was when Misato showed up and saved Shinji's buttocks and began their classical journey to Nerv's underground base.

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At Nerv's main command center...

A man whose heart was colder than stone stood next to the reinforced glass wall that separated the command room from the chamber that held Evangelion Unit 01. This was the man who summoned Shinji for his own evil deeds. His name: Gendo Ikari.

To his side was his ever constant shadow and second in command: Kozo Fuyutsuki. Though that he often aided Gendo, Fuyutsuki was easily more human that his superior. But despite this, the elder man could easily be as ruthless as Gendo was. But Fuyutsuki did have a heart, unlike his ruthless boss.

But there was a third man with them. He was an older man, several years older than even Fuyutsuki. But he had aged well, the man was only had a few wrinkles on his brow and cheeks. His hair had dulled to a light silver that was combed back. He was dressed in a silk black suit, nothing fancy like an Armani, more of a simple dark business suit with a charcoal gray tie and black leather shoes. But as a contrast to his dark clothing, the elder man had a face that was kind and gentle. But his kindness did not hinder his performance, he was an elected government official, a senator, that was here to check out Nerv for his fellow colleges in the capital. The man had a determine and warmhearted charm that made it seem impossible not to trust him. "So when will your... son arrive?" The government official spoke with a hint of disgust at the thought of even considering Gendo as a father.

The tone of his words was not lost on Gendo. He turned towards the elder man and nearly growled at him, but held it back. It was one thing to have to deal with SEELE, but having to handle a simple government legislation member was quite another. The combination of the man's silver- tongued way of talking and charisma made him very difficult to handle. On a personal note, Gendo would rather deal with SEELE everyday than have to handle that weak hearted man. "According to the front desk, Captain Misato and the Third Child had arrived over twenty minutes ago. They should be here any minute."

"So the world's only hope rests on his shoulders?" He shook his head to show his sadness. "A child should not have to burden that responsibility."

Gendo responded. "It is irreverent, Shinji is the Third Child. He will pilot the Eva. If not, than all of humanity is doomed."

Fuyutsuki nodded in his head in agreement. "He is quite right senator. Ikari's son is the only chance for the world to survive." Fuyutsuki's firm lips twisted into a somewhat sardonic grin. "Why don't you go fetch him for us if you are so worried about the Third Child?"

The senator nodded and left the command center to join Dr. Ritsuko Akagi in the search for the missing Misato and Shinji. Getting lost in the Nerv maze was infinitely better than being in the same room with Gendo.

Several minutes later, Misato was still leading Shinji deeper into the corridors and farther away from their desired location. They were just passing by a door when it opened up to reveal Ritsuko and the kind old man.

"RITS!" Mistato bounced up and gave her best friend a grateful smile.

Ritsuko rolled her eyes. "Lost again? Do you realize the severity of the situation? The Third Angel has arrived!" Dr. Akagi was more than prepared to unleash a verbal storm when the senator cut her off by placing his warm hand gently on her shoulder.

"Now Dr. Akagi, she did not mean to be lost." He chuckled. "I remember when I first showed up last week, it took me over an hour just to find a vender machine to snack on. I think it is quite understandable that she would be a little bit behind."

"Thank you senator," Misato beamed cheerfully. The senator was listed as good people in her book!

The senator returned the smile to the captain before glancing down at Shinji and patting his head. "So you're the one huh?" He kneeled down and looked the boy in the eyes. "It's a pleasure to meet you Mr. Ikari. Your mother was the finest person I had ever known."

Shinji gasped. "You knew my mom?"

He nodded. "Yes, she was the most caring and beautiful woman I had ever laid eyes on. Whenever we would meet, she would talk about you for hours. She loved you more than life itself," he added on a final note.

Shinji found himself lost on words to reply with. "T-th-thank you, senator..."

With that, Dr. Akagi lead the three to the storage chamber to Eva Unit One.

"WHAAA! GIANT FACE!" Poor Shinji nearly had a heart attack when he saw the giant mecha. He began thumbing though the pamphlet he was given to by Misato in the hope of finding some information about it.

Ritsuko shook her head. "You won't find anything about it in there. This is humanity's last hope, the synthetic live form known as Evangelion. They are mankind's only hope against the angels."

Shinji was still somewhat shaken by sight before him. "And this is why I'm here?"

"Correct!" came a voice from above.

"FATHER!"

"It's been a while." Gendo spoke without a single hint of emotion.

Shinji had been dreading this moment ever since he received the letter from his father. The younger Ikari looked up towards his father and shuddered at his cold glare. Shinji turned away, lacking the strength to say what he had been wanting to say ever since Gendo abandoned him all those years ago.

Behind the glass, Gendo lips turned into a horrid grin. His son was as weak as he always was.

The senator saw Gendo's cold smirk from the ground and placed a supportive hand on Shinji's shoulders.

Gendo ignored the old man's gesture towards his son. "We're moving out."

"What?" gasped Misato. "Unit Zero is still in cryostasis! Wait a minute! You're gonna use Unit One?" Misato dreaded what she realized the true reason why she brought Shinji here.

"There's no other choice," reassured Ritsuko to her worried friend.

"Now wait! Rei can't do it yet can she? We don't have a pilot!" cried Misato. She was hoping that poor Shinji wouldn't be the one.

"We just received one," responded Ritsuko.

The senator glared at her, his anger showing in his gaze. Ritsuko ignored him. "Shinji Ikari, you will pilot it."

"NOOOOOOO!" All eyes turned towards Shinji. "I-I-I won't pilot it..." he whispered, nearly too quiet for anyone to hear him. Shinji looked up towards his father. "Is this why I'm here? You just want to use me!"

Gendo nodded and spoke in an even, emotionless tone. "That is your purpose. You are here to pilot the Evangelion, nothing more."

Shinji was close to tears when he felt a warm hand on his shoulder. Looking up, he found himself staring into the gentle eyes of the senator and found a renewed determination to resist his father. "You heard me, I won't pilot it..." he spoke above a coarse whisper, only loud enough for the gentle man to hear it.

"Very well Mr. Ikari," he nodded. "I understand and respect your wishes." He looked up towards Gendo and shook his head to tell Gendo his son's choice.

Gendo turned to the monitors, telling his subordinate his latest order. "Wake up Rei."

"Can we use her?"

"She's not dead yet." Gendo said heartlessly.

"Understood," the man answered and connected the monitor to Rei.'

"Rei? Our spare is unusable. You will do it again."

"Yes sir," came a weak and frail voice on the other side.

A moment later, a set of nurses wheeled the battered and bruise Rei up towards the Eva, moaning all the way in pain.

Shinji's eyes were wide in absolute horror at the sight in front of him. Unknown to him, his own hand gripped the elder man's own.

The senator looked up towards Gendo though his class wall and growled. It wasn't right that the fate of the world rested on this monster, but that is the way things were. Though that didn't mean he wasn't going to stand by and do nothing.

But before he could react, the base trembled as if a bomb had detonated. All around, crewmen stumbled in a wild fashion as the base continued to rock and to Shinji's utmost horror, the injured Rei was thrown off her hospital gurney and landed roughly on the floor. He broke away from the senator and was by her side to held steadied her. Shinji peered in her red eyes and felt ashamed that he would allow this girl to be placed in danger. No... it wasn't him. It was his father! That monster did this to everyone! Not once caring about the pain he inflicted.

Another explosion rattled the base, this one knocking a giant metal beam from the ceiling free. The massive object went on a straight drop down right above the two children. The senator's eyes went wide and without a moment's thought dove for the child and making himself into a pathetic human shield. It was obvious that they wouldn't live but perhaps his added protection might be enough to save their lives.

Fortunately that was when Unit One's arm broke free of its liquid containment and intercepted the falling beam.

"THAT'S IMPOSSIBLE! UNIT ONE'S RESTRAINS ARE STILL ON!" Poor Dr. Akagi looked like she was about to suffer a heart attack.

Shinji ignored the doctor's panicked attitude and continued to stare into the dull red eyes of Rei. Within those crimson circles was nothing but simple acknowledgement of his presence. It simple did not matter to the girl that he trying to help her.

Shinji felt a warm pair of hands holding his shoulders. He looked behind and faced the senator. "Shinji, I know you're scared," his voice was gentle and kind. "And you have every right to be scared. All your life, you've been abused and abandon, unloved by anyone except your departed mother, and now you've been asked to save the entire world when no one ever helped you. But you must consider something important Shinji. When it comes down to it, which is more important? The crosses we bear, or the way we bear them?"

Shinji bowed his head at the thoughtful words and made the right decision. "I'll pilot it, sir."

"Good man," the senator smiled genuinely.

Within moments, Shinji was placed in the Entry Plug and injected into the Evangelion. While up in the control room, things were moving at a hectic pace. The bridge crew of Aoba, Maya, and Mokoto worked in a fever pace setting the settings for the launch. Misato was at the helm, giving out orders to them while Ritsuko monitored the Eva and its effects on the pilot. The only people who seemed not to do anything were Gendo, Fuyutsuki, and the senator. They all stayed silent as they watched the drama unfold.

Gendo glanced over to the senator. "Your job of convincing the Third Child to pilot the Eva was commendable," he spoke in a thankless tone.

The senator glared. "What I did, I did for him. So take whatever thanks you've got and stuff it!"

Fuyutsuki choose that moment to intervene. "Careful senator. Remember that you are here only to observe, not participate."

The senator choose not to respond as Misato gave the final order. "EVANGELION UNIT ONE! LAUNCH!"

With those words, Shinji and Unit One were launched up the shaft onto what was left of Tokyo 3. Shinji tried to calm himself and follow Ritsuko's advice on how to handle the Evangelion. Sadly, Shinji tripped after his first step and landed unceremoniously on the ground. He got up again and continued on towards the Third Angel.

As Shinji finally got his first look at his opponent, fear began building in his heart. This thing was like a monster from nightmares that he suffered from every night. Shinji gulped as any strength he felt he had from the Eva leave him.

That was when the Angel attacked.

The Angel made his first moved and grabbed the Eva by the face. It lifted Unit One off the ground while its arms suddenly swelled up. The monster than gripped the Eva's arm and twisted it violently.

Shinji let out an agonizing scream.

"Clam down! That's not your real arm!" reassured Misato.

"Where are his defense systems?" cried Ritsuko to the bridge crew.

"The system's not responding!" Maya cried desperately.

"His field's not up! It's not unfolding!" Makoto cried out.

"It's not up?!" yelled a panicked Ritsuko.

The angel crushed the Eva's arm, breaking it in two jagged pieces.

"Left arm damaged!" cried Maya.

"The circuits have snapped!" said Aoba.

Shinji was moaning softly inside the cockpit as the Angel lifted him higher into the air. The purple protrusion on the Angel's arm lengthen before slamming forward though a hole in its hand and smashing into the Eva's face.

"AARRRRR!" Shinji screamed again from within the Evangelion.

Within seconds, the face armor of the Eva shattered into pieces. The Angel followed though by slamming the Unit One into the side of a building while the monstrous Angel charged up another energy beam from its claws and impaled the Eva in the head.

"NO!" cried Misato as a massive amount of fluid burst through the front and back of the Eva's head.

"Unit One has gone completely silent!" said one of the male technicians.

"Misato!" cried Ritsuko.

"ABORT THE OPERATION! EJECT THE ENTRY PLUG AND DISPATCH EVA RESCURE!

"We can't! The system's not responding!" said Maya.

"WHAT?!" yelled Misato in shock.

The Eva slowly twitched as it laid on the ground. Even though life still flowed though Shinji, he was in no condition to continue. Sadly, the Angel wasn't about to leave him alive and so it continued the attack.

First it grabbed the Eva, lifting it over its head into the sky. As if he was presenting it to the Lord himself as a sacrificial offering. Next the Angel brought the Eva down and slammed its back on its knee, making Shinji feel as if his back was broken. Then it began slamming Unit One repeatedly on the ground over and over again in a horrifying pattern. Each slam made Shinji believe that another rib was breaking. Finally, to top the horrid combo off, the Angel tossed the robot though several condemned buildings, which caused each of the constructions to instantly collapsed.

Inside the command room, Gendo glared at the screen of the massacre over his steeple fingers. Something's wrong... he thought. Yui should have gone berserk by now. Surly she's seen the horrors I've put Shinji through, so why hasn't she reacted as the MAGI predicted? Though Gendo hated to admit it, only one choice was possible. Something is restricting Yui from taking control and instead allowing the Third Child to continue to pilot. If we survive this, I'll have to find out what is forcing her to remain inactive. Gendo looked up towards Misato. "Captain, prepare an immediate evacuation."

All eyes turned towards Gendo at what he just said.

Fuyutsuki spoke up. "That is unnecessary commander. You said it yourself: 'If Shinji fails than all humanity is doomed.'"

Gendo glared at his subordinate before issuing commands. "We will have Rei pilot Unit Zero to combat the Angel. Captain, make the necessary adjustments."

"What about Shinji?" Misato pleaded. She didn't have a clue what to do to help the poor boy.

"If he isn't dead yet, he will be in a minute. Hopefully the Angel will take enough time killing him for us to prepare Rei."

Everyone in the room fell silent at the plan except for the senator. He rushed up towards the communication system. "Can he still receive outside communications?" he asked to Maya in a hurried tone.

"Y-Yes sir!"

"Patch me though!" he ordered.

Gendo was about to order the senator's arrest when he heard Shinji's voice whimpered from the intercom. "N-no more... please... no more..."

The senator's knuckles whiten from the tight grip on the microphone. But despite the physical stresses his body showed, his voice carried a cool, confident tone. "Shinji, the Angel is like any other beast. Simply damage it enough and it will fall. Attack where you feel it is most vulnerable and you'll succeed."

"YOU STILL HAVE FAITH IN HIM?!" screamed Fuyutsuki. "HE'S ALL BUT DEAD!"

"I have faith in him because I know he'll win," he spoke fiercely, daring any to challenge him. It did not slip pass Gendo's notice that he was pressing the button on the intercom, allowing Shinji to hear his words.

A very clever way to boost Shinji's confidence, Gendo thought.

Within Unit One, Shinji took in the senator's confident words. Faith, that man actually had faith in him... Even Misato herself doubted he'd do it, but not the senator. For the first time since his mother died, someone had believed in him even though all hope seemed lost. He spoke in his radio. "I won't fail senator." His tone was final and exact, showing no fear whatsoever.

The Angel moved closer towards the battered Unit One. It stood in front of the fallen Eva and straightened both its arms. Behind them, twin pillars of energy extended along with the Angel taking aim at the cockpit of his opponent. Time seemed to slow down as information began to make its way to Shinji. His legs were useless, unable to even stand on his own. However, even with one arm damage, he could still use his hands. The Angel's only weapon was the pulse generators on its arms, other than that, it was pretty much defenseless. Its stomach contained little mass to protect its organs, so a strong enough attack there would easily finish it.

All this Shinji knew in an instant.

With a final burst of hidden strength, Shinji grabbed the Angel's hands and covered them with his own along with twisting its long arms backwards just as the energy was about to release. The monster panicked and automatically launched its attack, thus propelling the Eva forward with inhuman velocity towards the Angel. With a gut-wrenching screech, the Evangelion tore though the Angel's belly, spilling its organs and bile along the streets of Tokyo 3. Without its s2 organ intact within the safe confines of its belly, the Angel erupted into a massive explosion. The sky burned in crimson fury over the city of Tokyo 3.

"SHINJI!" cried Misato from the safety of Nerv's command center. Everyone, even Gendo himself, was shocked when Shinji used the Angel's own attack to slingshot him though the alien's own body.

Gendo reassumed command. "Is there any signals being received from Unit One?" he asked the bridge crew.

"N-none sir," whispered Maya. Never in her life had she seen such a desperate maneuver used before.

Gendo continued on. "Dispatch the workers to return Unit One to base."

"What about... the pilot?" Misato asked as she continued watching the explosion.

"He is irreverent. All that matters is that the Eva is readied for the next encounter," he spoke coldly.

Misato felt readied to cry. "Shinji..."

She felt a hand placed on her should and found that it belonged to the senator. "There is no need for that dear, look at the screen."

All in the command room looked to where he was pointing. They saw a trashed up Eva, crawling on all fours, slowly making its way back to base. What looked to be blood formed trail behind the Evangelion due to the massive wounds and tares on its chest, face, and now his hands. The Unit's outer casing was burnt and blacken to the point of unrecognizing. All in all, it looked like Shinji went to Hell and back. Considering the blazing inferno he crawled out of, that statement wasn't that far off.

Misato beamed. "Contact Eva Rescue and tell them to have a full medical team ready!"

"Acknowledge," replied Aoba as he radio the medical wing of Nerv.

Gendo turned to leave. "Fuyutsuki, I leave this to you."

"Yes sir."

As Gendo made his way to the exit door, he looked back towards the senator. Something told him that that man was going to be trouble for him and his plans. Pushing the thought aside, Gendo left. SEELE needed to be informed of the latest development.

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The next day...

Shinji awoke to the typical Nerv ceiling in the medical wing. He groaned as a shiver of pain ran down his body. Never before in his life had he underwent such physical agony. Looking over to the side, he noticed that the kind senator was sitting in a chair, looking fairly exhausted.

Shinji smiled. "Thank you for everything sir," he whispered.

He blinked tiredly, like he hadn't slept in days. He blinked several more times while rubbing his eyes. He glanced at the sore Shinji. "Finally awake my good man? I'm glad. You've really put a scare into Capt. Misato, you know?"

Shinji nodded, which caused another moan from moving his battered body again. "I had to do it sir. If I didn't, than you and the others would have..." Shinji found himself at a lost. He couldn't bring himself to say the last word.

"Died?" the senator finished. "But we didn't. And do you know why? It's all because of you Shinji. You saved us all. So thank you Shinji, thank you for your everything you've done."

Shinji found himself close to the point of tears. "I couldn't have done it without you senator. We make the perfect team!"

The kind old man chuckled. "What a brilliant idea Shinji." He smiled honestly. "All it would take is a little guidance and you would be unstoppable. You need little help from me though, I can tell you are destine for great things."

Shinji found himself to the point of tears. So it wasn't too hard to imagine that some would be traveling down his face. Never before had he meet anyone who cared for him so much. His voice started cracking as tears started running down his face. "T-thank you... Senator Palpatine."

Not the end. Only the beginning...

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Mwahahahahahahah! A MAD MAN! I'M A MAD MAN! BWAHAHAHAH! First I turned Carrot Glace into the Green Goblin and now I'm turning Shini into a Sith!

(Author recomposes himself) And it's due to Ian McDiarmand awesome portrayal of the senator from Naboo. As I said in my bio, I want to do fics that have never been done. There are countless Shinji-with-a-spine fanfics out there and the majority follow this plotline: Shinji shows up in Tokyo 3 and swears to he'll kill his father. Next, he hits on Misato during the car ride and acts really intelligent. Once he arrives at Nerv, he openly refuses to pilot and manages to piss off Gendo big time. So when Rei is pulled out, Shinji won't let her pilot the Eva and he kicks the fannies of any guards Gendo sends after him. Than Shinji shows his heroic side, gets in the Eva and proceeds to kick angelic ass! Finally the whole thing is topped off with Shinji getting jiggy with it with every female in the series but his mom.

Now, I'm not saying that all those fics are bad. Those are my favorite types of NGE fanfics. I'm just saying that it's a bad idea to be repetitive. Todd McFarline said it best: 'The fastest way to bore yourself is to keep telling the same joke.'

Now for the big question: Why a Sith? And my answer: Why not?

This all started when I started wondering who was the sneakier badguy: Gendo Ikari or Darth Sidious? One guy was able to fool 12 smelly old men in a dark room and whose biggest aspiration was just to be with his dead wife, while the other massacred the Jedi Order and conquered the entire galaxy. (rolls back eyes) Oh yeah, real tough decision.

Another reason was ever since I did my Darth Maul/Sailor Moon crossover fic 'Of Siths and Sailors' I've been wanting to do an anime crossover with each Sith. The Darth Maul story was easy since it was just an action packed fic while the Sidious storyarch will be more intrigued with espionage suspense. But don't worry, once Shinji gets his lightsaber, it's gonna be bloody! (heh heh heh) Sadly though, I haven't really seen all of the Evangelion series. I just saw DVD #1 for rent at a Video World and I thought it be pretty cool to watch on a weekend. So I really don't have a clue how the story goes. That's why I'm trying to find a website that pretty much tells what happens in each episode and possible shows pictures from each episode.

But this won't be a fic showing the same old storyline. The bulk of the chapters will be Shinji receiving his Sith training and Palpatine maneuvering everything to follow his nefarious plans. My goal with Shinji is to turn him into an amalgam of all three of Sidious's other Apprentices: The savage fury and skill of Maul, the charisma and charm of Tyranus in his secret identity, and top it all off with the cold evil of Vader. Scares the Hell out of me just thinking it! (double heh heh heh)