A/N: The second installment to fixing the most infamous Evangelion series.

Reborn:
The story begins as done in the original story.....
Fourteen years after the worldwide cataclysm called Third Impact, the scene takes place in Earth's orbit, where Asuka Langley Shikinami and Mari Illustrious Makinami, pilots of the Evangelion mecha, are sent by a mysterious new Commander to intercept a top secret escort where four Evangelion prototypes are revealed to be Agents of NERV, their greatest enemy.  They are Black Armored Evas, but with multiple red glowing spider eyes on their faces where two of them have scythes and the others pair holding long ranged weaponry. Their names in this movie are Unit 07, Unit 08, Unit 07.2, and Unit 08.2.

Currently, they were carrying an adrift, dormant Eva in Earth's orbit. With a massive gaping hole in it's chest where a spear used to be and containing the same classic features both Asuka and Mari instantly recognized: The Infamous Unit 01.

The pilots are informed the Eva would be brought towards the Moon after a series of calculations based on their observations, after finally being brought out of hiding during all of these years. But it must be recovered if they are to ensure another Impact does not occur to wipe out Humanity completely. Asuka and Mari would be launched out into space as Asuka still slightly argues with Mari (who barely listens to her anymore and merely brushes her words off unless it was something important), both in Unit 02 and the newly constructed Evangelion.
Unit 04.

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(This would be briefly mentioned by Mari upon her short argument with Asuka during their launch into space: The first Unit 04 would've still disappeared mysteriously along with NERV's US Branch installation from a possible accident involving the use of the Fourth Angel's recovered S2 engine, Shamshel. But out of mysterious circumstances involving the aftermath of Third Impact, Unit 04 resurfaced and was recovered to officially be listed as an active Evangelion Unit with herself as it's pilot)

They both use their AT Fields to generate a new ability with new devices installed temporarily: Invisibility Cloak. They use it to sneak upon the four unsuspecting Eva Angel drones, planning to take them out silently and retrieve Unit 01. The mysterious group supervising the Two Evas, watching before they were both caught by their AT Fields (activated partially in a Phased Array Radar mode for extra defense) made contact with the other two AT Fields, thus exposing them out of their camouflage. Now left out in the open, Asuka instinctively attacks and leads the charge with a shout. While Mari is ordered to help her out and she agrees, knowing there's no option left but to fight.

Both Units go into an intense battle, Mari and Asuka managing to work together while putting aside their differences in order to fight back against the Four Angel Evas. Two of them using their scythes or AT Fields in close combat and the other two, using their lasers or arsenal of weapons to attack from distances. Unit 02 would be given a Giant Riot Shield to block out all of the Angel/Eva pair's barrages of laser and bullet fire, from a rocket launched into space and labeled, 'WILLE' while Unit 04 is given two Massive Boxing cannons that can be worn like gauntlets and fire explosive fire while punching it's foes, from another rocket with the same name.

Asuka would block Mari and provide her partner, cover as Unit 04 rushes at the other two Eva/Angels, battling the two and managing to kill one of them by exposing their gut armor, shoving both drilling muzzles into the Eva/Angel's stomach and launching herself back while blasting a large gaping hole through, blowing it up in half. Leaving the other one to slice one of the gauntlets off Unit 04's hand and beat it around as Mari attempts to counter with her other gauntlet and try to embrace full synchronization with the Eva, even shouting at it several times to help her out.

One of the supervisors in an undisclosed location would reveal that the Eva has yet to awaken itself and open up to the pilot like Unit 02 has done already with her pilot, despite many failed attempts to synchronize with it until now. They can only hope things don't go become worse as the battle continues. As Asuka's shield began to weaken, Unit 04's large metal container worn on it's back as well as another on Unit 02's back, a Battery Pack, suddenly deactivates after running out of power and now the Eva is limited to five minutes (as stated by a technician in the undisclosed location). Mari angrily rushes at the Angel/Eva, taking out a Prog Knife out of one of 04's shoulder columns with the other available hand and stabs through the Angel/Eva's AT Field to penetrate through, blow up the head by punching it hard with an explosive headshot, and has Asuka bring the Unit back to her so the White/Red Eva could launch itself from the riot shield and fly at the two remaining Angel/Evas, using full power to dash behind them, destroy blow both of them up and sending them over to Unit 02 right before Unit 04 powers down at the same time.

The Red Eva's Battery Pack would also shut down and instantly switch to it's own Internal Battery, leaving Asuka to suddenly dash forward while ditching the now useless shield to fight them head on. Shooting spikes into one of their heads despite their faster regenerative abilities, tearing one of their arms off, Eva02 seemed to finally win when it sliced one's head off with both her Prog Knives and then ripped a weapon off the third one's arm to blow a hole in the Last Angel/Eva's head, just seconds before shutting down. That was when, from the horror of both the pilots and the supervisors, all Angel/Evas began to regenerate back to their full health and were about to finish off the Units.

That was when, suddenly, a familiar roar is heard and two bright lights shine the dark space above the Mortal Earth. The return of God.

"RAAAAAAAAAAAAAAAAA!"
Unit 01 awakened with a mighty inhuman roar, regenerated it's large wound and proceeded to brutally destroy the Angel/Evas with relative ease, luckily without the need to unleash a greater power it has used against the 11th Angel, Zeruel. It then deactivates and descends back to Earth, leaving military forces of unknown identification, to retrieve Unit 01 as well as the other two Units. A mysterious person watches from inside another undisclosed location, similar to an Eva cockpit showing full screen of the Earth's night sky with Eva01 falling and says he has been waiting for Shinji.

Cue intro

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Hours have passed since the battle has taken place. It is still nighttime where a mysterious battleship-like silhouette is floating an oceanic lake of red blood-like water, surrounded by a landscape of ice. With a smaller fleet of aircraft carriers and battleships.

Inside the Giant, slightly deformed battleship, a person was slowly waking up from his sleep, groaning as he found himself in a strange medical room. It was Shinji in a patient gown, who already was shocked from the feeling of a black collar worn tightly around his neck and several nurses treating him as if he was some monster.

Then he spotted Asuka and tried to plead to her what was going on, only to see her punch the bulletproof glass and glare at him with her death eyes before leaving. Even Mari, the one sister figure he always looked up to, passed by without saying a single word in a pink colored Plug Suit and wore a jacket as well. She never even looked at him as they both wore their jackets and left to god knows where. He would be introduced to at least someone who was kind to him, Sakura Suzuhara. Toji's sister, who was a medical
officer and gave him a physical exam while informing him that her brother is alright; the only thing she could tell him without getting in trouble. This was shortly before Shinji was soon tied to the bed and sent to the Command Deck, without anyone telling him as he tried to resist and begged to know what was going on.

Ounce he was taken there, all he could see was a darker, smaller command center with red windows and holographic screens showing the night sky. More than three people were working as technicians for the command center compared to NERV' HQ and he still tried to beg what was going on, despite SOME explanations from the stranger staff and crew like in the original movie. Only to discover a horrifying familiar face.

His former caretaker and supervisor for the Evangelions, "Admiral" Misato Katsuragi.

Along with others who completely took him by surprise by their new looks. Maya, who looked like a man when he first saw her, Ritsuko with shorter hair who gave him his SDAT player, and even the other two staff members he remembered from NERV, were just fainted memories of what they used to be. He tried to plead to Misato and ask what's going on. She only took off her glasses and said, "Shinji Ikari.... For now on, you will be doing..... (glares down at him) Nothing."

Much to Shinji's horror, Ritsuko states that the collar worn around him is an explosive collar and if he pilots any Eva again due to Third Impact (which still prevents any Eva pilot from aging), it'll detonate and kill him before he has the chance to start another Impact. While Kaji's fate is unknown, as told that it doesn't matter by Asuka and that he's KIA by an unknown staff member who also treats him coldly, Unit 01 is discovered to be trapped in a bony cage like the other two Evas, for the sake of only research and to find out why NERV still desires to use it. The Eva is in tighter bonds contrasted to the other two Evas, in order to prevent it from going Berserk.

The organization, Misato leads is called WILLE: A Rebel Militia composed of Humanity's surviving remnants from Third Impact and founded to not only save what is left of humanity, but to destroy it's previous employer NERV. The paramilitary organization that turned on everyone when it's secrets are leaked out after Third Impact and declared war ever since. But Misato doesn't inform the boy about this.

Outside of the giant battleship, an army of drones are launched by NERV to attack the fleet, Ritsuko believing that they came to retrieve Unit 01 and probably the Third Child as well. Misato has Shinji returned to his "cell" in an escort by two soldiers and a nurse. Before she launches the flying battleship Wunder, powered by five N2 fusion reactors and a different Magi System called the Magi Achiral, to destroy them. Shinji, unfortunately, learns from one of his guards that the other previous occupant of Unit 01, Rei Ayanami, was never found.

Mari and Asuka would sit back as Misato gives the order to deploy a mass swarm of man made machines, the TRIDENT Fighters. Or in other names, the "Country Crawlers."

They're piloted by people who are selected for standard avian combat, instead of Evangelion combat like the Organization's Eva pilots. So the pilots in the Docking Bays holding dozens of rows of the Giant Tanks, climb down their individual ladders and enter the machine. One certain pilot stopping for a moment and glancing down at a very deep trench to see Shinji being transported through a horizontal, seen through glass elevator. Before the pilot went back to climbing down the ladder, entering their own Trident and closing the hatch above them. Their engines activated as their headlights turned on, their machinery adjusting into Active Mode to release their arms as two large hatch doors opened. Before the clamps for each one released, all Fighters launched out of the Giant Battleship to fly up into the sky and open up their turrets and weaponry. Before they gun down the drones as they clash against NERV in a Dogfight. While the giant battleship, the AAA Wunder, switches into Attack Mode and enters the battle.

(This is the turning point of the movie into becoming significantly different)
When the crew inside the Wunder are seen again, the real current appearances of the crew are revealed.

(The other crew members look exactly the same when compared to their original counterparts, while Mari has a White and Red Plug suit to match her Eva instead of Pink)

Misato tells Ritsuko that she hopes Shinji will be safe in his quarantine cell, not wanting to lose him again and risk failing into protecting him from causing another Impact that will kill everyone. With Ritsuko assuring her that the Tracking Collar Device will pinpoint his current location if he pilots an Eva, as they told Shinji (despite all of them noticing that he seemed to space out and look at them as if they were monsters).
Asuka still makes the same insult about Shinji being too stupid to run away again as she narrows both her eyes and puts her hands behind her head, while Mari says nothing and focuses her attention on the drones. Even if she is still the same age, she has long matured to focus in the War they have yet to win against her former superiors.

The battle is completely one sided in WILLEs' favor, where only one Trident is downed by the drones before they were completely wiped out by the combined forces of the Wunder's fleet and TRIDENT forces gunning them down. Just as everyone inside the Wunder (except Shinji) and the fleet began to celebrate, Makoto and Shigeru would suddenly report an unidentified bogey heading straight to them at more than 180 m an hour. Misato orders the image to be zoomed in at the direction, the unknown source is coming from in and they are all shocked to see a familiar face they thought they would never face. An elegant warrior capable of thwarting a power not even they could stop, fourteen years ago. A warrior Mari and Asuka has nightmares because of It being the cause for Shinji's possible death until they found him alive.

The very being they thought would never be on NERV' side.
Enter: The Ultimate Soldier, Evangelion Unit 06.

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The Mysterious Eva dashes towards the Fleet with it's divine flight, not seen using any equipment or jetpacks their Evas needed for flight. Ritsuko indicated this was indeed the Eva that immobilized Unit 01 to prevent it's completion into executing Third Impact, and now wants Unit 01 for possibly NERV' reasons. Misato quickly orders the two pilots to get into their Evas immediately, as the TRIDENT squadron are dispatched to shoot down Mark 06. But the Eva only flies past them, taking all of their bullets unscathed and swings it's arms open wide as an invisible force pushes the entire TRIDENT squadron apart, causing most of them to crash into each other and explode upon impact. The Eva would fly around in the air, avoiding all of the missiles and cannon fire shot by the fleet and remaining Mechas. It even had the missiles follow it before flying straight down towards the Wunder, flying back up at the last second as the missiles would be too late to diverge. Thus flying into the Wunder, only to blow up on it's AT Field instead.

Maya would report that there are no damages caused by the missile barrage and after witnessing the Eva destroy most of the Mechas in midair, Misato quickly orders a full retreat, causing the remaining Mechas to fall back into the gigantic flying Battleship. While the battleships cease fire to avoid attention and gaining the risk of casualties. Both Unit 02 and 04 are launched out of the Wunder, using jet packs to fly while connected to their own Umbilical Cables to remain active for prolonged periods of time. "Let's do this!" Asuka exclaimed, feeling eager to take down the Eva.
"Fourth Child, standing by!" Mari exclaimed, two hatches in the ship's roof opening up to shoot out rifles for Unit 04 and 02 to catch into their arms before pumping them. "Locked and loaded!" Both exclaimed.
"Begin the attack!" Misato ordered.

The moment Unit 06 spotted them, one of it's shoulder columns opening up to reveal a standard Prog Knife. It pulls it out, swings the knife forward and suddenly causes the blade to transform, lengthening rapidly into a Progressive Katana.
The Two Units shoot at the Eva as the Wunder unleashes an all out attack. Unit 06 would raise its other hand, summoning a powerful AT Field to block all of their attacks. Which even Ritsuko pointed out, that the AT Field shouldn't be this powerful to endure their strongest AT-piercing rounds and shells.

Then, Unit 06 proceeded to dispel the Field and suddenly swings the Blade in the air, causing an invisible force to suddenly slice the Evas' weapons in half, including all of the flying Battleship's turrets. The ship's surface exploded as the Evas suffered deep cuts into their armor, both pilots yelping in pain and Shigeru reporting that 94.2% of their  mobile defenses have been destroyed. The two Evas, meanwhile, are forced to resort to their Prog Knives and dash forward, Unit 06 activates it's AT Field to turn it into an offensive form of energy, the same Unit 01 has done before and launched it straight at the Duo.

Launching them both crashing into the ship and causing the Wunder to violently rumble for a few seconds. Inside the Ship, Sakura and the two guards braced themselves while holding the bed in place so it doesn't move. But Shinji could care less.... He was so confused, overwhelmed and full of guilt as he could now remember what has happened all these years ago.

Meanwhile on Deck, Makoto reported another anonymous attacker coming from their right. But when the screens were put up to reveal what the surveillance was currently recording, there was no one there. Shigeru identified the attacker's location: The Red Ocean of LCL.
Suddenly, a series of explosions burst into crosses of Red Light from underwater, stabbing half of the battleships and all submarines into the air before exploding in the air. A second Eva emerges from the bloody ocean waters to reveal itself as a New Enemy of WILLE,
Evangelion Unit 09.

The Evangelion proceeded to assault the remaining fleet attacking it, using it's four winged-like jet pack limbs to block all conventional weaponry from the battleships and fighter jets launched from several air cruisers. After using a Pallet Rifle to destroy the fleet and it's own superior strength, it spares the air cruisers and transforms it's back limbs into a giant jet pack to fly up to the Wunder.

The AT Field on the ship would be activated, only for Unit 09 to pierce right through with it's own Prog Knife. Then proceeding to tear into the battleship's armor with it's own bare hands. Misato would inform the pilots of Unit 09 attempting to infiltrate the ship, interrupting the two Units as they struggled to fight Unit 06, especially when it had superior combat skills and already destroyed their Prog Knives with it's Prog Katana, sliced through their AT Fields and constantly beat both of them up as proven from their fractured armor and visors. Unit 02 quickly turned to fly down to the bottom of the Wunder and intercept Unit 09. Unit 06, however, elbowed Unit 04 in the face behind it and spun to kick the White Eva high into the air, then swings it's katana in the air to slice off both Unit 04's Umbilical Cable and the Jetpack.

Mari would scream in pain while her Unit is falling out of the sky, but quickly place the Eva's feet on the jetpack and launch off of it so it could grab ahold of the Cable's severed end that was still hanging loose on the Wunder. While it had only 5 minutes left and proceeded to climb up, Unit 06 dashed at Unit 02 and kicked her into the ship's tail satellite before she could reach Unit 09.

The Red Eva gets up after falling into a destroyed satellite dish and dashed at the Eva, trying to get a hit on it with her Second Prog Knife. Only to be blocked, each time Unit 06 uses it's Prog Katana. Then, Unit 06 stabbed it's Prog Katana into the second satellite dish behind it and proceeds to beat the living hell out of Unit 02, using karate combos to rapidly punch it's face, kick to break several limbs and used IP Man's Chain Punch before knocking Unit 02 off her feet by bashing her in the face with merely the Eva's palm.

Unit 09 would break into the Wunder, reach into the Evangelion complex and find Eva01 tightly secured in one of the Wunder's cages. It would proceed to cut the cage and shackles open with it's Prog Knife, the pilot inside informing their associate that they are currently breaking the second target free. A male voice would respond calmly as he is busy toying with Unit 02 inside the cockpit of the Mysterious Eva, adding that he will rescue the first target very soon.

Unit 06 would wait for Unit 02 to get up and dash at him as Asuka angrily uses it's second Prog Knife to lunge at it. Only for Unit 06 yo catch the hand, twist and break the hand and takes the knife to slice open the Red Eva's throat as blood shat out, stabbed it in the head and grabbed the Eva to throw it behind it, the body intentionally thrown at the White Eva that just got back on top of the Wunder's roof. Unit 04 dodges the body, takes another Prog Knife from it's other shoulder column and jumps high into the air as only 4 seconds were left. Unit 06 would grab it's Prog Katana by the handle, slice it up through the  second satellite dish to take it out and jump up high into the air as well, ending the battle with a sudden AT-enhanced slash across the top. Slicing both limbs and head right off of Unit 04, before it turns to transfer the AT Field into it's free hand and launched Unit 04's body into the right wing of the Wunder, breaking it as the battleship suddenly falls out of balance.

Everyone inside, tries to brace themselves. The crew, the engineers, some casualties were shown with several standard pilots and tactical engineers falling off of platforms as they screamed in horror. Luckily, Sakura already locked the group and herself inside the quarantine room to only land on the glass wall, ounce they came back in. Shinji was already untied to the bed at that time, so they only panicked from the ship seemingly falling out of the sky.

Ounce it crashes it's tilted side into the Seas, Unit 06 was already making it's descent to the right spot and tore it's way into the approximate location, tearing a wall off the quarantine room by the time Misato, Ritsuko and a group of guards came in to rescue them. At first, Shinji was terrified at the sight of Mark 06 and screamed in horror as did Sakura. However, in his perspective.... He heard the Eva call out, "Shinji." in Rei's voice as it lends it's free giant hand to let Shinji climb onto it's palm.

Shinji gasped in surprise, asking out loud, "Rei?"
"Rei!?" Sakura asked in response, unable to believe what he was saying. "Shinji, what are you talking about?! That cannot be possible! Whoever can be piloting the Eva is not Rei-"
She was interrupted by Misato, who told her to quiet for a moment and shouted to get Shinji's attention. While Ritsuko was silent in confusion, unable to tell why Shinji asked for Rei's name when Shinji and everyone else in the room only heard a male voice speak from the Eva's speakers.

"Come along with me, Shinji. There is not much time." Rei spoke again in Shinji's head, making him smile and try to climb. "Rei! I knew you were alive-!"
He was suddenly stopped by the guards, who threatened to shoot him before Misato told them to stand down with an angry shout. In Shinji's perspective, it was only a calm order, similar to his father's usual tone. "Shinji, I need you to listen to me! The organization, WILLE is trying to save everyone! I am trying to save everyone, including you! If you go with that thing, whoever is working for NERV.....! You'll be killed! Including everyone! Please, Shinji! You have to listen to me! I promise we'll find Rei! I promise we can do everything we can to save whoever's left with your help, but joining this Eva will not help you! Please, I'm begging you!"

Meanwhile, in Shinji's perspective...... He only heard the complete opposite that made him look down with a shadowed look on his face. "No. Never. You're not the Misato I remembered all those years ago, none of you are....."
Misato widened her eyes, unable to tell what he was talking about. But it was too late, he had already jumped into the Eva's hand and the Mysterious Eva proceeded to jump off the Wunder to float in the sky while Sakura already begged him not to go, gently opening it's Entry Plug and opening the hatch automatically to let Shinji hop inside before the hatch closed, Entry Plug inserted back into the Eva's back and soon Unit 06 flying off.

With Unit 09 jumping out of the broken Wunder with Unit 01 in it's arms and takes off after Unit 06. But not before it reached the Magi System in the Ship's core and stabbed an Entry Plug-like weapon into the large mainframe connecting all three Magi, leaving it behind as glowing red ooze proceeded to leak into the circuit boards from the Entry Plug's openings and assimilate the hundreds of wires and circuits inside. 

Inside Mark 06's cockpit, Shinji leans forward as he expressed his relief about finally being able to see Rei safe again-
Suddenly, his eyes are seeing what he didn't expect to see. A silver haired, taller boy in a Black Plug suit as he hummed to himself.

He then looks over his shoulder and smiled softly towards him. "We see each other at last, Shinji Ikari. It is nice to meet you."

Meanwhile, Misato and Ritsuko are seen walking together as thousands of men around them are doing their best to repair damages of their machinery, torn and crushed infrastructure, and fixing some power outages. Both of them arguing that Shinji may be suffering hallucinations, ounce saying in shock that he has an explosive choker on them repeatedly, even when Ritsuko stated to him twice that he only has a tracking device she built, that could also shock him into unconsciousness if he were to go too far in piloting an Eva again on his own. Misato refuses to believe that he's going crazy, but Ritsuko says that isn't what she means and that he might be suffering some possible form of trauma he developed from his discovery of causing Third Impact.

Just as they walk back into the Command Center, Misato is given a status report: The communications are down to only an hour delay of making contact with the outside world where other bases of WILLE are located, the Evas and ship's relies will cost most of their mechanical supplies to restore completely, and their forces have depleted to only a small amount. But at least the pilots are both alive and conscious while being currently recovered into their own medical rooms to be given medical treatment from almost dying of shock, much to Misato's relief. 

Ritsuko states that although they're aware Shinji would never harm anyone, they must've been desperate to take both him and Unit 01 since he might be used as an intentional weapon to bring about a Fourth Impact. Makoto commenting that as they were just about to spend some time in ensuring Shinji is mentally safe, able to be trusted and properly informed of all the events that occurred since Third Impact, things only went down for the worse.

Misato would feel guilty, knowing it was her fault to believe Shinji would be able to take this all in without any possible mental illness and not have them suffer the consequences. Now he's gone and there was nothing they could do about it, again. Ritsuko promises they'll get him back, even though she's against her wishes since it's best that they keep Shinji from being used as a means to completing NERV' ultimate goal.

Suddenly, their computers are hacked with red screens, the staff being unable to regain control as they report a mysterious virus attacking the Magi System. Ritsuko and Misato looks up at the main screen, horrified to discover a Stowaway onboard. A computer virus, in the form of red hexagons taking over black hexagons into the Magi System. 

"This can't be. Computer viruses don't work like that!" Shigeru spoke, the entire crew thinking the same thing as Ritsuko and Misato glared at this. "This is no ordinary virus."
"Long time no see..... Angel." Misato spoke, small reports of Angel DNA patterns showing up in the computer besides revealing a series of hexagons being taken over by red hexagons.

By none other than the Virus installed in the ship by Unit 09, the stowaway that is a nano-sized version of their Long Forgotten Enemy.

The Fifteenth Angel, Ireul.

To be continued..........