A/N: Part 2 of Evangelion 3.33 You Can (Not) Redo.

Reborn:

The Second Act begins in the ruins of Tokyo-3, where Unit 06 would slowly descend into the center of the crater and travel down the penetrated inner tunnels of Central Dogma's remains with Unit 09 by it's side while carrying Eva 01, all while Shinji was horrified at the sight of what was left of the Geofront and was confused of what happened to all of this. What the hell happened?, he thought. And what was even happening? And who exactly was this person with him in the cockpit to an Eva he had never seen before? Just too many questions stirred into his mind, but he mustered up the ability to wait. They soon descended deeper below the tunnels and making it's way into the only place intact, the one place Shinji recognized to be where Misato ounce took him a while back.
Terminal Dogma.

They enter the area with no issue, due to being allowed to enter as the doors to Terminal Dogma would open after the grey haired child, stated his success of rescuing the Third Child on the intercom.
Unit 09 would proceed to fly down with Eva01 while Unit 06 would slowly hover to the skeletal landscape, causing Shinji to be slightly disturbed by how so many things have changed while he was gone. "Welcome home, Shinji." A familiar deep voice had spoken, snapping Shinji out of his thoughts and confusing him.
"Father?"

Soon, the Black/Orange Eva would land as Unit 09 took Eva 01 to another, unknown section of Terminal Dogma that opened upon the Eva's presence. It would head to the main platform where Shinji ounce walked on to see where the headless white Giant laid, reaching out for something while standing on all fours in a room full of giant human skulls instead of LCL. Shinji would ask what happened to the Angel they guarded and the calm stranger would say politely, "The Angel is now a carcass and can no longer provide the LCL that is required to breathe in as you would pilot the Children of Adam. As a result, all of the blood it has ever shed are now dried bones and marrow. A graveyard for these unborn Lilin in a way."

Shinji would be confused of Adam and the term such as 'Lilin,' but he's interrupted when Mark 06 takes a knee to take a closer look down below. And Shinji couldn't help but find it hard to recognize a familiar man. His father, Gendo Ikari.

He would openly welcome his son while sounding colder than before as he stood before the kneeling Eva. He tells Shinji that he is back here to pilot Unit 01 against the remaining Angels that have been said to return by ancient records they have used to predict Angel awakenings, the Dead Sea Scrolls. Not only that, he is to, soon, pilot Unit 01's replacement known as Unit 13 with the pilot who rescued him, Kaworu Nagisa, in order to enact the final phase of NERV. Shinji would use the intercom to ask why and what has been happening, but Gendo says nothing. He would only respond that he is to fulfill his role as a pilot of NERV and get it done without questioning.

As of this moment, a new Angel is said to arrive at any moment and Shinji would first be sent out to dispatch the threat in order to refresh his experiences in piloting an Eva. Although Shinji remembered how this went exactly like the first time they met in years the first time he fought an Angel, but this time.... He's not refusing this time. Although he wises to know what is happening.... He just feels like a tool to them anyway. Doing tasks and following orders without hesitation.

An old alarm would go off, leaving Gendo to say, "Our time is up. Prepare the Third Child for combat, Kaworu. You will stand by as backup incase he fails."
"Yes sir." Kaworu says calmly with a simple nod and has his Unit rise back up to it's full height. Before making his way way towards the massive entrance where they came from and has the Unit ascend back to the surface.

Shinji would be silent the whole time, feeling gloomy over the entire situation. Not even caring what happens to him at the moment, only thinking about what happened to everyone and especially........Rei.

He was interrupted by Kaworu's humming, who would apologize to him for singing again and say that he couldn't help it. "Music is the greatest achievement of the Lilin culture." He glances over his shoulder with his smile. "Don't you think so? First Lieutenant Ikari."
"You know my rank?" Shinji asked, surprised that someone still remembers a rank he earned for his services in fighting all previous angels before the Tenth.
"Everyone knows your rank. Pardon me if I sound rude, but you should be more aware of your position."

"You think so?" Shinji tilts his head, leaving him to nod and glance back to pay attention to where he was going. As Unit 06 made his way to the surface, Shinji would awkwardly clear his throat and ask, "Kaworu Nagisa.... That is your name, right?"
"Please, call me Kaworu. I honestly prefer we skip the formalities, Shinji Ikari."
Shinji blushes. "W-Well in that case, you can just call me Shinji."

Kaworu chuckles this and would say it is a pleasure to finally meet him face to face before offering a hand shake. They both shake hands as Unit 06 reaches out into the surface and there, they see a giant black orb, floating towards the Geofront crater. Shinji asks how he can defeat this new Angel if he doesn't fight it with Unit 01. Since his Eva was taken away by someone else, but Kaworu replies that it was only taken away to receive repairs. He was confused, right before Unit 09 flies out behind them to place Unit 01 on it's feet, seemingly repaired and back to perfect condition. It was practically good as new, which left Shinji in awe by the fact how it was so quickly fixed. He could've sworn there was a massive gaping hole in it's chest for some reason, but Kaworu would have his Unit approach 01 and have the entry plug come out so that it could open the hatch automatically and has it's hand open wide below the Entry plug. Shinji would reluctantly jump out as some LCL poured out, then be gently taken into a manually opened entry plug of Unit 01 and placed inside after Shinji had to manually open the hatch himself and close it on his way inside.

Unit 06 would retract it's entry plug as did Unit 01, before leaving with Unit 09 to let Shinji do his job as he synchronizes with the Eva, the child still feeling a bit uncomfortable to be piloting the same weapon that both helped him fight back.... And harm people.

He would be interrupted by the Black Orb, where he ends up trying to rush at it with an aggressive shout. Still believing that he only has five minutes left in his Eva's battery before it powers down without an Umbilical Cable to keep it online for a prolonged period of time. The black orb would stop ounce the Unit rushes at it, even grabbing a Pallet Rifle out of a rusted building that struggled to pop out of the blood soaked floor fast enough. An AT Field would appear in front of the black orb, only to get quickly penetrated by the Eva's rifle billets and then pierce right into the black glassy surface. Shards broke off, the entire orb cracking as the Eva would jump at it and smash it's foot into the face of the orb. Completely destroying the glass case and revealing the Angel.

The Sixteenth Angel, Israfel.

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The much larger Angel would instantly unwrap it's arms from it's around it's shoulders and cross slash through the rifle, slicing it in half before firing a laser out of it's eyes that blasts Eva01 miles away from it.
Although it didn't damage the Eva, it still burned like hell to Shinji and only aggravated him to fighting back harder. He would jump back up as the Angel slowly leaps into the air and falls down to slash at his Eva with it's claws, but he had Unit 01 dash to the side with her superior speed and knock it down with a punch and spinning kick to the back. She took out the Prog Knife and would slash off the Angel's right arm when it got up to try and backhand her, trade blows with the knife against Israfel's other claw and chop off the arm before jumping up to slashing straight down, cutting the entire Angel in half and slicing through the Red Core like butter.

"I.... I did it!" Shinji exclaimed, feeling proud for killing an Angel on his own and just before the Eva could shut down. Unfortunately, that was not the end of it when the two halves began to move. Suddenly beginning to grow out their own halves and limbs, forming to become differently colored clones and regenerated into separate bodies that matches Eva01's height while having their own Red Cores.

"Oh you've got to be f-" Shinji grunted as he felt his face get punched hard when the Angels punched Eva01 in the face and sent him flying down the purple crater, losing his Prog Knife in the process.

As the Eva rolled a dozen times, the Angels would jump down and slide fast by the Eva's sides. Eva 01 would get back on her feet and slide down while trying to fight back, but due to their cooperative combat overpowering only one Unit, she is easily beaten and clawed repeatedly without barely having a chance to fight back. She would get slammed into the ground and dragged towards one of the exposed flaps of the crater's center, thrown against the bloodied wall and fire lasers at Eva01. Shinji shouted in anger as he would summon an AT Field of his own, blocking both of their lasers and only obscuring his view from the smoke. One of the Angels dash at the Eva, but gets it's arm grabbed by the Eva. Just like he tried to do with the last Angel he faced, he successfully places a foot on it's face and pushes it back before instantly tearing out it's core, crushing it in the process.

The Angel would fall limp on it's back as blood shot out of it's gaping hole, while the other one dashes at her and the Unit suddenly jumps off the wall behind her to leap over the Angel, letting it crash into the wall instead. Just as Eva01 landed at the other side and turned to face them, the other Angel stabbed it's arms into it's dead comrade's body, merging them into the body and was seen transferring some of it's flesh inside it's arms into the corpse, suddenly causing it to regenerate it's injury and regrow a new Red Core. Then the arms separate from the revived Angel and grabs it's arms, jumps over it and launches it's comrade as a projectile to tackle Eva01 to the ground. The Angel proceeded to beat up the Unit, rapidly punching and stabbing the Unit's face or neck using it's claws. Shinji did the best to fight back and was about to succeed until the other Angel joins in by jumping into it's comrade, fusing back into their original form and grabbing the unit by the head with one arm to slam her into the ground repeatedly. Until it throws it into the air, then blasts the Unit high into the air with it's laser beam.

After the Unit would crash straight into the ground outside of the crater, the giant Angel would float out and approach the Unit, about to finish her off by jumping high above it and flying down to use it's claws while dividing into two. Until suddenly, they were stopped by an invisible force and lifted into the sky above in an instant, Mark 06 coming in just in time to use it's AT Field (by raising it's hand) in lifting them afloat while preventing them from escaping it's powerful hold. It would close it's hand, shrinking the AT Field into a tighter space and forcing the two to fuse back together. Before an N2 missile is fired at them from Mark 09 using an Rocket Launcher close by, blowing up the Angel entirely.

Then two black orbs would fall down onto remains of bloody buildings, which Mark 09 would approach to pick them up. And as ordered by Gendo, the Eva would try to squeeze them tightly and crush them in it's grip. Only to fail when the Cores have used all of their energy to make an extremely hard surface and ultimately have enough resistance to endure the Eva's strength. A female voice inside the Eva's cockpit would report that she is unable to crush them and then ordered by Gendo to leave them alone so the Angels will recover and be destroyed later while their cores are vulnerable at that time. She complies and drops them, walking away while Kaworu would stare at the Eva. Showing somewhat of a smile towards his comrade before turning back to Eva01.

Later, Shinji would be in a dark room while wearing casual clothes, sitting on a chair with rows of dusty, empty chairs next to or behind him as Kaworu sat next to him in a relaxed form. "Clearly, you're not proud to see yourself resulting in a situation such as this." Fuyutsuki would state as he has an old projector reveal an image of the most recent taken image of the incident after the Angels' temporary defeat.

The Eva half buried into the literal, bloody ground and humiliated in it's defeat by the Angels. Fuyutsuki would then scorn Shinji for losing to the Angel's tactics and not being able to adapt to their fighting style before they attempted to kill him. Although he should be hard on him, he expresses that he honestly shouldn't blame the child. He's been only asleep for fourteen years and despite being in some sort of cryostasis sleep inside his Eva, he might've love a lot of skills from either a ton of stress or he hasn't even focused properly because he's going through so much.

Gendo suggested that he should be revoked of his privilege to pilot Unit 01 and simply have the Unit be controlled using a much stronger, modified Dummy Plug System they have developed since the events of the 11th Angel. But he tells Shinji that he believes he'll do better than last time and recommends that he trains with Kaworu to whip himself back into shape. While Kaworu was fine with this, Shinji was still taking it hard and only nodded in response.
He then had the other pilot come in, needing her to escort him to his room while he has a word with Kaworu for the time being. When Shinji would glance to his left, he gasped at the sight of a familiar face. Rei, who was wearing a black Plug suit labeled, "09."

"REI!" He would dash at her and hug her tightly in his arms. But all she would do is barely react to him, standing with barely any emotion on her face. She would ask him to let go of her with a monotone voice, leaving him surprised and lets go of her. "Rei, it's me! Shinji! Don't you remember!?"
She stared at him emotionlessly, only answering that she knows who he is but she has no memory involving any encounters or interactions with him her whole life.

Shinji couldn't believe what she was saying. He begged Fuyutsuki and Kaworu if she was just having amnesia, that she doesn't truly not have any memories with him being her friend after all of the things they did together. Beating the Fifth Angel, helping defeat the Ninth Angel, visit Lake Ashi in a pirate ship, visit a hot springs district, rode the ropeway up to the top of Komagatake to see the sunset and even shared-
"I am sorry, but I don't have any memory of this. It's best to drop it so I can take you to your room sooner than later." Rei advises him, but then grabbed by the shoulders. "Please Rei! You have to remember! PLEASE-!" He gets slapped in the face and instantly let go to back off, holding his face as Rei held her hand up. Rei would only lower her arm and advise him to follow her, before walking out. With Shinji saying nothing since and soon follows her out.

While exploring Central Dogma, Shinji further finds that Rei has no memory of Shinji, little understanding of the world, and only does what she is ordered. Shinji concludes that she is not "his" Rei. She would take him to his room and then leave, having other duties to perform.

Shinji would sit in his room, alone (without his SDAT player since it wasn't given back to him), until Kaworu would finally be finished with his meeting with Fuyutsuki and arrive to his room without the Third Child expecting him. He asks Shinji to come with him, as he wanted to show him something that he might enjoy and distraught, the boy decided to join him and see what he had to offer.

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He takes him to play a piano duet to play in a large white room with a young tree by their side. And although Shinji found it a little hard to play a piano, Kaworu kindly taught him how to play, encouraging the boy to learn and as he began to learn how to use the keys, he became confident and plays faster the more he plays it. During which, the two bonded together.

After their piano lesson, Kaworu would then gift him a school shirt of Toji's, revealing that he found this abandoned in the school Shinji used to go to shortly before the events of the world's devastation. Shinji would be distressed by this, now reminded of whatever had happened to the world and why this was the case. Deciding to disregard orders from Gendo in keeping this a secret, he takes Shinji out into an exposed platform in the Geofront Pyramid and reveals to him a fully scaled image of the current world. 

Where the Moon and Earth's surfaces are both covered in red crosses and bloody surfaces, the terrain being overrun by red crystals shaped like Evangelions and the Moon no longer being tidally locked. Instead, it was much closer with clouds on it due to now having it's own atmosphere and the oceans no longer having tides.
Shinji would be feeling more shocked by the current state of the world, Kaworu revealing that ever since he fought the Angel known as Zeruel, Unit 01 absorbed it's blood in order to "rescue" Rei and gained the powers of a God during it's awakening. And ever since it evolved to become Godly, it triggered an semi-complete version of Third Impact, resulting in the world in long story short. And the reason for why he is still at his age as he was fourteen years ago since the event, there has been a side effect from Third Impact that has a curse placed on all Eva pilots that practically render them immortal from aging, including himself.

He also explains the nature of NERV's Human Instrumentality Project, to Shinji's horror: By killing all life on Earth, new life that bears the "Fruit of Life" can be created. And Shinji was doing exactly what they desired, until he put an end to it and stopped Unit 01 from finishing everyone off by neutralizing it with the Spear of Cassius, an ancient weapon greater than both Lances that came with the Black Moon and White Moon to keep their Angels immobile incase any errors occurred. Shinji would question what the Two Moons are and he responded, "Why, the Vessels for the First and Second Angel of course. Adam and Lilith. Terminal Dogma and the Geofront are the very centers of the Black Moon."

Shinji would gasp at this. "Y-You mean-"
"Yes, the headquarters of NERV and Tokyo-3 was Lilith's Vessel all along. A derelict that was used to bring Lilith from the stars and crash down upon Adam's property, that being your world." Kaworu replied, not only revealing what they've been protecting this whole time, but revealing..... That Adam was literally, the First Angel to arrive on Earth and had the right to create his own life before Lilith's arrival, which indicated that even humanity were not originally Earthlings. Only extraterrestrials themselves.

He added that an accident occurred according to the Dead Sea Scrolls and the Black Moon crashed on the same planet as the White Moon, which violated the First Ancestral Race's code of laws, the progenitors of the two vessels and extinct race that sent many vessels across the universe in order to preserve their dying race. Their code stated that only one Angel can live on a single planet and create it's own life from their vessel's Tree of Life, so the two Lances of Longinus from both separate vessels, which were constructed to destroy any errors that would cause the extinction of both angels and the world they live on, incapacitated them and forced them into a state of dormancy. While Adam's children would be prevented from awakening until the results of Second Impact, Lilith's blood would leak from her body (which he says the Lilin call LCL) and eventually form into Lilin.

Shinji had at least some questions answered, but they were replaced by an even larger amount of questions. He tried to ask as many as he could, but Kaworu stated he couldn't tell him too much. Otherwise, the child will just be stressed out from the harsh truths and he expressed concern over Shinji's stress with a smile. Shinji would only blush a bit and look away in shame while saying, "S-Sorry, I didn't mean to go that far...."
"It's quite alright. The Lilin are always known to be curious and emotional over anything they learn about. I wouldn't mind because the way they react to many things... I always found it to be fascinating." Kaworu chuckled.

Shinji would be a bit confused of who he was talking about, the "Lilin" and Kaworu only responded that that is the name he came up with for Lilith's offspring, which he believes is a preferable name for a species he believes to be the Eighteenth Angel. A being of many, with no physical power like the Children of Adam but makes up for it with knowledge and inner AT Fields from Lilith's Tree of Life, which is their individuality and ability to create their own souls. Which always interested him, due to how wisely they have used their power to evolve to such great lengths as a civilization and even mimic the power of Adam's Children with that of the Evangelions.

"I.... I see." Shinji responded, now finding it much easier to see the bigger picture and why Misato was so insistent in him saving humanity and why they would keep Lilith in NERV in the first place, especially why Adam's Children might be wanting to merge with Lilith. They just want their home back, and they were so close to getting it back thanks to him. He felt even more distressed at that thought, as that only ever happened because he was just trying to save Rei.

He even says to Kaworu that he didn't mean to cause all of this, to have everyone he ever knew turn against him for ruining the world and making things harder for them to save what's left of humanity. Kaworu stated, "That's not how the Lilin sees things... But then again, their stubbornness to accept some truths could lead them to such irrational actions. For example, your DSS collar."

Shinji would look down at the collar and touch it with his fingers, still finding the chilling thought of inevitable death to be disturbing. As they could kill him with the explosive device the next time, they ever see him again. He asks if Rei, the Rei he knows and has risked everything to save..... is still alive. And everything he did wasn't pointless.

Kaworu would take a moment to process this out of wonder, as he placed a finger on his chin. He wasn't quite sure himself, as he guesses the Rei Shinji cared for, might be dead and alive. Possibly in limbo within Unit 01, the remains of Zeruel or perhaps in the Chamber of Guf, a place where all souls of the Lilin go and stay until the end of time, which Unit 01 opened during the beginning of Near Third Impact. He adds that perhaps Shinji's actions might not be in vain, as they could probably bring her back if he continues serving NERV. If he continues to fight the Angels and maybe even initiate their plans of Instrumentality with Unit 13, he just reunite with her. After all, Kaworu was the one who stopped Unit 01 from completing Third Impact is so he could save Shinji from all of the misery he would bring upon himself and show him happiness.

If he accomplishes this by helping Shinji bring back the one person he still cares about, he'll be satisfied. Shinji would smile widely at this, thanking him for everything he's done and has yet to do for him. He would say that he honestly has no idea how he could repay him, but Kaworu only smiles and says, "All you have to do is repay me with your kindness and cooperation."

Rei, meanwhile, rests in a tank of LCL, where she is currently resting alone within a dark and wide room instead of resting on a bed at her former room.

At first, things seemed to be fine. Her mind was empty, no feelings to distract her and no other issues to contribute to taking her focus. That was until..... A female voice began to cry out for her.

Ayanami......

Ayanami.....

Ayanami!

She would open her eyes wide, no longer in the Dummy Plug Tank and instead finding herself in an unfamiliar cockpit while wearing a white plug suit labeled, "00." She was inside Eva01, as the Unit was standing in a testing room besides Unit 00.
"Ok, Rei. We're going to initiate the Testing Run.  Before we start, I need you to let me know when you're ready." A much younger Misato said, standing  besides a much younger Ritsuko and the three technicians in a room opposite to the Evas with only a large window to see them. With her long purple hair let out and wearing the same clothes she used to wear as Ritsuko had only less wrinkles and the same lab coat she would always wear.

Rei wouldn't answer and look around instead, confused of what was happening and why she was in this Eva instead of her tank. "Rei?" Misato asked, catching Rei's attention again as she faced her front to glance at the window from the other side. "Where am I? How did I get here?" The short haired girl questioned in her monotone voice, leaving Misato and Ritsuko to raise their eyebrows. "You're in a Plug Testing Room to experiment with your synchronization rate in Unit 01. Shinji's doing the same thing in your Eva too." Misato responded.

"Is something the matter? You should be fully aware of the purpose in this test." Ritsuko asked, sounding a bit suspicious in Rei's intercom. "What day is it?" Rei asked instead of answering the question. Both women were even more confused, but were starting to come up with what was happening with her. "It's Sunday. It's only been a week since you both defeated the Fifth Angel." Misato responded.
"Fifth......Angel?" Rei looks down, trying to process when that has ever happened. And now that she thought about it, that happened way back into the past. But that didn't make any sense. "Are you ok, Ayanami?" A male voice asks as a small holographic screen pops up in front of her, revealed to be Shinji in his blue plug suit labeled, "01."

He seemed genuinely concerned for her, but she only stared at him with her same blank expression. "I am fine."
"We should cut the test short. It's not you to lose memory of the situation as soon as you entered Unit 01." Ritsuko spoke in the intercom, which left Rei to suddenly glance back to her front. "No, I am alright.... I only needed to refresh my memory. That's all."

Silence was only given to her in her own perspective, but both women decided to go with it after a moment of consideration. "Very well then. Shinji, stand by and wait for your turn."
"Right." The holographic picture of Shinji disappears and Rei stared at the window as Misato asked, "Ready?"
"Yes." 

"Very well. Initiate Sync test." Ritsuko spoke before the lighting in Rei's 360 screen lit up and obscured her vision of the room outside of her Eva, now turning into the form of a rainbow.

As this happens, she stared into the colorful abyss for the longest time. The screen pausing at this moment for more than 30 seconds as Rei did nothing else and only showed emptiness in return at the empty environment in her surroundings.
Then she began to see more strange apparitions around her as someone else, sounding just like her, began to express a poem.

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Mountains, heavy are the mountains
But that changes, with the passage of time
Sky, blue sky, what your eyes can't see, what your eyes can see
The sun, one, only one
Water, it is agreeable, Commander Ikari
Flowers, so many the same, so many without purpose
Sky, sky of red, red the color, the color I hate

Liquid flows, it drips, ripples, and pours
Blood, scent of blood, woman who does not bleed
From the red soil the humans come

Humans made by man and woman
City, a human creation
Eva, a human creation as well
What are humans?
Are they creations of God?
Humans, that which is created by humans
This is that which is mine
My life, my heart
I am a vessel for my thoughts
The entry plug, the throne of the soul
Who is this? This is me

Who am I? What am I? What am I? What am I?
I am I.
This object that is, is myself
That which forms me
This is the self that can be seen, and yet this is not like that which is myself
A strange feeling
My body feels as if it is melting
I can no longer see myself
My form, my shape fades from view
Awareness dawns of someone who is not me
Who is here? There? Beyond me, here
Shinji

This person I know, Colonel Katsuragi

Dr. Akagi

People, my classmates
The pilot of Unit Two

Commander Ikari

Who are you? Who are you? Who are you?

She would open her eyes at the last vision, and glance around, now finding herself back in her LCL tank and with no one around. Wondering if this was real, she glanced to her front and saw a sudden glimpse of herself in a school uniform, who stared at her with no emotion. She widened her eyes a bit, then blinked and there she was gone. Vanished as quickly as it appeared.
Then she would look down and wonder if that was just a dream or something really was happening and she couldn't read it what was it.

'It's been happening for two weeks now.... Who was she?... Who am I?..... Who am I to be doing this to myself and why?....' She thought to herself and then slowly closes her eyes, sleeping ounce again.