WARRIORS OF THE REPUBLIC
by Gunman

Disclaimer: I do not own Evangelion, Star Wars The Clone Wars, or their characters.

Summary: When Shinji and Misato get pulled through the 12th Angel to another galaxy, they end up fighting alongside the Jedi Knights and Clone Troopers against the evil Separatists.

NOTICE! THIS CHAPTER HAS BEEN COMPLETELY REWRITTEN!

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Shinji.... I'm not going to let you die! Misato thought as she stared down at the large shadow-like 12th Angel that had consumed nearly the entire city from the transport helicopter.

"Major! We've got a transmission from Commander Ikari of NERV!" Makoto Hyuga shouted next to the woman.

"Ignore it!" Misato shouted.

"But, Major!"

"NO! Hang up! I'm busy!" she shouted.

Misato knew that the Commander would have scuttled this rescue mission the second she had requested it. So in order to save her ward, Shinji Ikari the Third Child, she had requisitioned 10 special military transport helicopters for a daring mission: rescue Shinji!

Her plan was to use grappling cables to haul the massive Eva-01 from the shadowy depths to which it had sank in to. But to get to Unit 01, she'd also requisitioned a small N2 Mine, which she planned to use to weaken the Angel's defenses and hold on Unit 01. Then she'd use the chopper cables to haul Unit 01 out and back to safety. Of course, the whole thing hinged on Unit 01 not being blown to bits by the N2.

"Alright, people! Let's do this!" Misato shouted.

The N2 Mine was dropped directly into the Angel as the helicopters created a perimeter around the edges of the large shadow. The Mine exploded, causing a massive hole to open up inside the Angel. Fortunately, it was large enough that they could see the immobile Evangelion.

"Fire grappling cables!" Misato shouted to the other shoppers through her headset.

The choppers fired their cables at the purple robot, each one magnetically latching onto it. The head, the shoulders, the arms and the upper part of the chest.

"We got it! Everyone pull!"

The choppers started to lift out.... only to suddenly stop with a jerk.

"What the... what's wrong?"

"We're getting resistence from the cables." the pilot said.

"It's the Angel! It's pulling Unit 01 back in." Makoto shouted.

"NO! You're not taking Shinji!" Misato shouted as she suddenly leaped out of the chopper and flew down the cable towards Unit 01.

"MAJOR!" Makoto shouted.

In a panic at knowing that the Angel was going to take Shinji and Unit 01, Misato made a judgement call. She would pull Shinji out of the entry plug and haul him back up using the chopper. Whatever happened after that would be left to Ritsuko to save the Eva. As she landed on the shoulder of the Eva, she quickly went over to the entry plug and found the control panel. Punching in the code for the manual release, Misato looked over and saw that the other cables were starting to snap and unhook from the surface of the Eva. She managed to get the entry plug ejected and open when the cable she had slid down snapped, the helicopter jerking backwards and flying off.

Misato was now more panicked. The Eva was sinking too fast for the chopper to return and retrieve Shinji and herself. So once again, Misato made a snap judgement. The second the entry plug was open, and saw that Shinji was alive, she pushed the boy back into the entry plug, got inside herself, and closed the hatch. Two seconds later, the head of the Eva was consumed by the black shadowy body of the Angel.

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"So... this is what the inside of an Evangelion is like. It's cozy." Misato said as she snuggled up against Shinji, practically sitting in his lap.

Shinji could only blush as Misato's body pressed up against his. His smug laughing fit over Misato coughing when she inhaled the LCL for the first time having past, he was now on the verge of a massive nosebleed. Mostly since Misato had once again forgotten to wear a bra today.

"You were right." she said.

"About what?" Shinji asked.

"The LCL. It does taste like blood."

"Told you." he said dryly.

Misato shifted to try and get herself more comfortable. Which only made Shinji more uncomfortable due to the confines of the entry plug.

"Good thing I'm not claustrophobic." she said.

"Misato?"

"Yes, Shinji-kun?"

"Thank you."

"For what? Being unable to save you? For getting trapped inside the entry plug with you? For nearly squishing you inside this cockpit? For taking up half the life support system's energy, which will probably kill us quicker?" she asked.

"For not abandoning me." he said.

Misato smiled as she pulled the boy into a tight hug.

"I couldn't, Shinji. You're my family." she said, her tear absorbed by the LCL.

Suddenly, a violent explosion shook the pair.

"Misato?"

"Sounds like they're going with Ritsuko's plan."

"Ritsuko's plan?"

"They're going to use all the N2 Mine's they've got to kill the Angel."

"With us still inside?" he gasped.

"They were planning to use them when it was just you."

"It was my father's plan. Wasn't it." he said, stating it more than questioning it.

"He approved it." Misato said. "The only thing he seemed to care about was getting Unit 01 back."

"Of course he did."

Their vision was filled by a blinding flash as both Shinji and Misato faded from their world.

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"Shinji! SHINJI, GOD DAMN IT, WAKE UP!" Misato shouted, shaking her young ward.

Shinji was awoken to an explosive exchange of laser fire and explosions. He looked around and gasped, seeing a scene that boggled his mind. To start with, both he and Misato were not inside the cramped entry plug of Unit 01. Instead they were in the middle of a large sand and rock gladiator-like arena where hundreds of people with laser swords were fighting against a seemingly endless number of skeleton-like robots with guns.

What's more, there were hundreds of giant humanoid insects flying around, many of the people with laser swords didn't look human, there were several other strange-looking robots coming out too, and there was a large green, spider/crab-like creature stomping around in the middle of the battle.

"M-Misato? What's going on?" Shinji asked, easily confused and shocked at what was going on around him.

"Shoot first, ask later!" Misato shouted as she quickly tossed him a strange looking laser gun, which she had gotten from a headless body in strange armor they had unexpectedly landed next to.

"What?" he gasped as he stared at the thin, long-barreled handgun.

"You know how to use that, right?" she asked.

"Uh..." Shinji said as he turned and saw one of the thin robots approach them, aiming it's rifle at Misato. He turned the gun on it and fired, blasting it in the head.

"Oh, good. You do." Misato said as she grabbed the rifle the droid had dropped and started firing as well. "Come on, Shinji-kun! Let's go!"

The scene was one of pure chaos as all around the battle intensified. Shinji, trusting his superior officer and guardian, stayed close to Misato and just kept shooting at the mechanical beings. It quickly became apparent to Shinji why Misato had taken up with the laser sword wielding people: they were defending both of them from the droids. Also, because he was shooting droids and not living people, Shinji had no hesitation about pulling the trigger.

In a way it felt like a video-game.

It would not have benefitted Shinji to learn that one of his shots had inadvertently caused one of the droids to fire wildly in the air before falling over. One of these wild shots flew up into the arena stands and struck a young boy named Boba in the head, killing him.

All around them, the laser-sword wielding Jedi Knights continued to deflect laser blasts and cut down both battle droids and super battle droids, uninterested right now as to who the mysterious pair were. They were just glad to have the help.

"Shinji! Follow me!" Misato shouted as she lead her ward over to where a group of insect-like creatures were using a massive gun-like device to blast the sword-wielding warriors. "Cover me!" She shouted as they blasted the creatures off the large gun turret and quickly took their places. The controls were obscure and difficult to understand, but the basic idea of how to fire a gun wasn't lost on a military minded person like Misato.

She turned the gun turret around and started firing green-energy volleys into the bulk of the droid army, destroying them in seconds.

While Misato continued firing at the droids, Shinji was watching her back. He kept firing at the droids but also at the insect-like creatures that were trying to take back their gun turret. Amazingly, he didn't seem to be missing as much as he thought he would. He was helped out in this by a pair of human beings, an attractive young woman in white carrying a laser rifle, and a young man with a long ponytail in black and brown robes carrying a laser sword.

"So... this is what you call a diplomatic solution?" the young man asked the woman.

"No, I call this aggressive negotiations." the woman in white said as she turned to Shinji. "Not that we're not grateful for your help, but just who are you?" she asked him.

"I'm Shinji." the boy said as he fired at another droid. "The woman firing the cannon is my guardian, Misato."

"I'm Padmé. This is Anakin." she said, indicating the young man who was blocking laser blasts with his laser sword.

"Welcome to Geonosis!" Anakin said as he deflected another laser blast back at a gray battle droid. "Hope you live long enough to see the rest of the galaxy."

"If we live through this, can you please tell me what the heck is going on?" Shinji asked as he shot down another insectoid.

"Sure thing!" Anakin shouted as he sliced at another humanoid insect.

The battle continued on and on, Misato firing the energy cannon again and again to decimate the droid army, a bearded man named Obi-Wan killing the large crab-like spider creature, and Shinji continuing to fire and hit his targets. However, this only bought them time as the heroic group of Jedi were eventually routed, the cannon turret destroyed and both Shinji and Misato now standing side-by-side with little more than three-dozen surviving Jedi Knights and one female senator.

"Master Windu, you have fought gallantly. Worthy of recognition in the archives of the Jedi Order." Count Dooku said from up on the stone balcony of the arena, pausing as if to bring dramatic emphasis to the situation. "But now... it is finished. Surrender and your lives will be spared."

"We will not be hostages to be bartered with, Dooku!" Mace Windu said defiantly.

"Then... I am sorry, my old friend." Dooku said, motioning for the droids to prepare to fire.

"Are we going to die, Misato?" Shinji asked his guardian.

"If we do... we die together." Misato said, clutching Shinji's hand with her free one.

Suddenly, Padmé looked up and shouted. "Look!"

Everyone's attention swiftly turned skyward as dozens of strange looking gunships flew into the arena from overhead.

"Well that's timing!" Misato grinned as the gunships, carrying sleek-looking, white-armored, T-shaped visor helmeted troopers, fired at the droids with their large blaster rifles. The droids fired back.

"Around the survivors, a perimeter create!" Yoda shouted from his gunship.

The battle joined once again, the Jedi Knights and Clone Troopers found themselves fighting side-by-side for both survival and victory. The survivors were quickly loaded into the landed gunships, along with Shinji and Misato, and evacuated into the air. Once they were airborne, the pair were given a good view of the wedge-shaped battle ships that were dropping off hundreds of thousands of troopers outside the arena into the surrounding desert area.

Shinji and Misato were flying high in their own gunships, apart from Anakin, Padmé and Obi-Wan, and staring down at what was like something out of a science-fiction movie.

"What did we get ourselves in to, Misato?" Shinji asked as he hung onto the inner handles of the gunship as it flew over the now joined battle against the advancing droid army.

"A whole other universe, Shinji-kun." Misato said, hugging the boy from behind as the gunship flew down to the assembly area. "And one that's at war, obviously."

On the ground, Shinji saw various squads of white armored troopers being lead by other Jedi Knights with their laser swords glowing brightly. Heading towards them at a furious pace, a mechanized army of droids and battle droids, but also the most twisted vehicles and robots he had ever seen.

Shinji and Misato were taken to the forward command center where a small greenish creature was standing and talking to a group of white armored troopers with different colored insignia's. Misato seemed to be rolling with things rather well.... but Shinji couldn't help but stare.

"Master Yoda, all forward positions are advancing!" the lead trooper said.

"Very good, commander. Very good." Yoda said.

"Is there anything we can do to help?" Misato asked as she jumped out of her gunship.

"And you are who, young one?" Yoda asked the woman.

"Major Misato Katsuragi, of NERV!" she said with a small salute.

"Heard I have not of this NERV. But military trained you are. Your help, we will need." Yoda said.

"Right." she nodded.

Misato quickly got into a tactics discussion with the lead trooper and the small creature called Yoda. It shocked Shinji that even after all they had been through, or maybe because of it, that Misato didn't seem that disturbed by alien creatures and robots with laser guns fighting all around them.

"Those giant metal spheres are rising into the air!" Misato shouted as she pointed to the Trade Federation ships that were taking off.

"Those are Trade Federation command ships!" the clone commander said.

"Those are space ships?" she gasped. "Do you have any long-rang cannons?" she asked.

"Commander, concentrate all laser artillery fire on the nearest starship!" Yoda shouted on Misato's suggestion.

"Yes sir!" the commander said, turning to the clones at the control panels. "Move all quadrants to sector 5-1-5."

Shinji just watched as the large laser cannons which were behind most of the advancing troopers, fired off energy beam after energy beam, striking and destroying at least two ships and causing them to crash back into the ground, sending up huge clouds of dust on the battlefield.

But while they did, the clone pilot that had brought the pairhe command center was calling for help.

"What's wrong?" Shinji, who was still in the gunship, asked the pilot.

"Receiving a call for assistance from the senator of Naboo." the pilot said.

"Senator? There's a senator in the middle of this battle?" he gasped.

"Yes, sir. Padmé Amidala."

"Padmé?" Shinji gasped. "We have to help her. Let's go!" he said, not really thinking about what he was actually saying.

"Yes, sir!" the clone said, and before Misato or Yoda knew what had happened, Shinji and seven clone troopers were flying off to help a woman whom Shinji had just met in a gun fight.

And naturally, a lingering doubt caught Shinji's mind.

Did he just call me 'Sir'? Shinji thought as the gunship took off at top speed.

Within seconds they were over their target.

"Over here!" Padmé shouted to the gunship.

The gunship quickly landed and picked up both Padmé and another clone trooper, adding to the other six they already had, not counting the pilot.

"Shinji?" Padmé gasped as she saw the boy with the clone troopers.

"Are you Senator Amidala?" Shinji asked as he helped the woman aboard the gunship.

"I am!" she shouted as the gunship took off.

"This day is just full of surprises!" Shinji said as the gunship took off.

Padmé directed the gunship to where Anakin and Obi-Wan had been following Dooku to. They arrived at the hanger, which had been carved into a small mountain, where Shinji, Padmé and the clone troopers leaped out onto the landing platform and raced inside. They arrived just as Anakin was battling against Count Dooku with two lightsabers.

The second they arrive, both Anakin and Dooku stop fighting.

"It's over, Dooku." Anakin said to the older man, motioning to the clone troopers who were aiming their weapons at Dooku himself.

"I don't think so, boy!" Dooku said as he suddenly blasted the floor with lightning from his hands, which caused the floor under Anakin to explode, sending him flying backwards into a wall.

"Stop him!" Padmé shouted to the clones.

The clones opened fire on Count Dooku, though Shinji was trying not to kill him. He leaped towards the other man in the room, the one with the beard called Obi-Wan, and slid across the floor as he fired his blaster. His intention was to get to Obi-Wan and cover him, which is why he missed Dooku several times, striking his ship instead. But one random shot finally got through, and blasted a strange device on Dooku's belt.

Using the Force, Dooku knocked the troopers back and quickly ran up into his ship before they could recover.

His personal vessel succeeded in escaping the planet, but the damage to the ship would eventually come into play, delaying Dooku's arrival on Coruscant by a full day. However, Dooku would sooner find out that Shinji's laser blast had damaged, beyond repair, the holographic projector with the Death Star space station plans.

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(Coruscant, Jedi Temple, 24 hours later)

"We can't thank you enough for all you've done for us." Jedi Master Mace Windu said to Misato and Shinji, who were now dressed in appropriate military-style uniforms to match the new titles they had been given. And naturally, Shinji's uniform had to be tailor-made.

"Yes." Obi-Wan Kenobi said. "If you hadn't arrived, who knows how things might have turned out."

"You're over-exaggerating, but you're welcome. Still, this war is just starting." Misato said. "I'll do all I can, but.... when this is all over, I need to find a way to get me and Shinji home."

"Of course." Obi-Wan said. "And the Jedi Order will help you in any way it can, Major."

As a result of their heroism and actions on Geonosis, both Misato and Shinji are inducted into the Army of the Republic against the Separatists. The war, dubbed The Clone Wars by many, started on Geonosis, and would soon spread to all of the Republic's neighboring systems, and even to the Outer Rim. The Republic had soldiers, but they needed commanders and generals.

Misato was quickly made a field commander for her tactical expertise. And naturally, in order to keep Shinji safe, insisted that her ward be made her lieutenant.

She smirked at how that conversation had gone.

(FLASHBACK, several hours ago)

"For your military background and expert tactical proficiency during the Battle of Geonosis, we're giving you the rank of Major." Chancellor Palpatine said to Misato.

"I was a Major. In my world." Misato said.

"So it'll be an easy transition here in ours." Obi-Wan said.

"As a result of your new rank, I am giving you command of the 108th Trooper Battalion. And your ward Shinji will be made a lieutenant." Palpatine said.

"Same as he was in our world." Misato said.

"I was What?" Shinji gasped, staring at the older woman.

"Uh.. did I forget to mention that?" she said sheepishly.

"You mean I had a rank? Was I even getting paid?"

"Yeah."

"Why didn't you ever tell me?"

"Well... I thought... you know... it was obvious."

"Apparently not enough."

Despite the growing seriousness of the upcoming Clone Wars, Obi-Wan and Mace just smiled at each other as the pair bantered back and forth.

(END FLASHBACK)

"However, there is something else we need to discuss." Obi-Wan said to the woman. "In private."

"Oh. Alright. Shinji, can you wait here?" Misato asked.

"Okay." Shinji said, sure that it was something that 'big people' needed to talk about.

While Shinji talked with Jedi Master's Yoda and Shaak Ti, Misato was taken out into the hallway where Master Windu and Obi-Wan started talking.

"So what did you want to talk to me about?" Misato asked.

"It's about your ward, Shinji." Mace said to her.

"Shinji? What about him?" she asked, instantly concerned.

"Has he been a little... unusual, as of late?" Obi-Wan asked.

"Uh... you mean aside from getting pulled here to this universe from another one? No." Misato said.

"What I mean is.... how proficient is he with a blaster?" the bearded Jedi asked.

"Not bad. He'll get better." she insisted.

"On Geonosis I noticed that he seemed to be a rather good shot, even to the point of not looking at his intended target." Obi-Wan explained.

Misato was getting a suspicious feeling about this. "What are you getting at?"

Mace and Obi-Wan looked at each other before turning to Misato.

"We suspect that Shinji might be a Jedi." the bald, dark-skinned Jedi said bluntly.

"A... Jedi? Like you?" Misato gasped.

"Not exactly." Obi-Wan said. "But he does appear to have 'some' Jedi traits. Such as the ability to see things before they happen. It's possible that these abilities could develop further."

Misato was now pondering this. Obi-Wan had given her a demonstration of the Jedi's Force powers earlier, and now they were telling her that Shinji could be one of them.

If she were any other person, she would have cracked up laughing like a loon. Actually, she would have, were it not for the serious expressions both Mace and Obi-Wan were wearing. And the fact that it was Shinji.

"So.... can you help him? Train him?" she asked.

"No. He's too old for Jedi training. The Code forbids it." Mace stated.

"However, we think we can help him... at least to develop this ability which would... quite possibly... save his life in battle." Obi-Wan said.

"Then Yes! Whatever it takes! If you can help Shinji, please! I..... I'm his guardian, but I can only do so much. If he can learn a new trick or talent or instinct that would save his life, and it's something I can't teach, then please... teach him!"

Mace and Obi-Wan looked at each other and nodded.

"We will do what we can. I promise." Obi-Wan said.

"But the most important thing for you to do right now... is not tell Shinji about this ability." Mace said to her.

"But why not?" Misato asked.

"Several reasons. The most important being: so he doesn't panic." Mace explained.

"Panic?"

"Master Windu is correct." Obi-Wan said. "If Shinji were to find out he has a strange new power, he will try to control it. That sort of thing, at his age, is very difficult, since all of our Jedi are trained right from birth. It could overwhelm him. On Geonosis he just used this foresight without being fully aware of it. As long as he accepts all this, as either luck or coincidence, he won't put himself in danger, or anyone else for that matter."

"Do you understand?" Mace asked the woman.

"I think so." Misato sighed. Another secret I have to keep from Shinji, but one he might find out about anyway. "For now... I'll keep this a secret." she said.

"Thank you, Major." Obi-Wan said. "And now... we have a war to fight."

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Author's Notes:

Just so everyone knows, the gun that Shinji has is Jango Fett's other blaster, the one that he lost when that three-horned monster beast trampled over him.

Also, this chapter was a little rushed. I was trying to get it uploaded on the first day of the year. I managed to successfully edit it to be better, so I hope everyone approves. This whole story was a long work in progress, and I'm still working on the other chapters. I've been working on it ever since I found out about the new Clone Wars movie and CGI-series. It's been a little hard to write this out, but I think I did a good job under the circumstances.

And just so everyone knows.... this will be a Shinji/Ahsoka pairing. I decided to write them up together because they are of similar ages, as well as opposite personalities, which could be a good attractor. However, Shinji won't meet Ahsoka until the next chapter, so for now you're just gonna have to be satisfied with this.

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OMAKE

"Master Windu, you have found very gallantly. Worthy or recognition in the archives of the Jedi Order. For centuries to come they will speak of this heroic last stand, each Jedi under your command fighting to the very last, never backing down from your foe even as you were routed and huddled together against the vicious onslaught of the mechanical army of the Separatists. From the farthest Outer Rim world, to the interior of Coruscant itself, will your names and deeds be written and remembered long after we have all been turned to dust and..."

"Oh, for gods sake! If you're to kill us, kill us! Don't bore us to death with your long winded gloating!" Misato snapped.

"I agree. Kill them now!" the Viceroy grumbled.

"Here, here." Obi-Wan said.

"Yes, Dooku, do us all a favor and stop the monologuing." Mace Windu said.

Dooku just rolled his eyes as they all said that. "Just because you don't have any drama in your souls.... or an education in the Shakespearean arts... doesn't mean that I can't try and give the best speech of my career!"

"Oh, just get on with it!" everyone groused.

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OMAKE 2

The droid army had surrounded the last of the Jedi and aimed their weapons preparing to fire. But just as they were prepared to fire, Padmé looked up and shouted, "Look Out!"

The Jedi and droids looked up and gasped as they saw a gigantic, purple behemoth suddenly appear out of thin air and fall back-first right down into the arena, crushing the thousands of battle droids in it's wake, it's head slamming into the balcony where Dooku and the others were, but leaving the Jedi and Padmé untouched right beneath the giant robots crotch.

The droids were crushed, Dooku and his Separatist leaders were dead, and the Jedi had survived.

From out of the entry plug emerged an LCL-soaked and soggy Shinji and Misato. They looked around and sighed.

"This is what I get for letting you teach me how to drive." Shinji said to this guardian.