Disclaimer: I don't own NGE, also this is the first time I'm writing anything, so advice is appreciated.

- Act I: Setting the Stage -

Chapter 1: Prologue

The sun shone down upon New York and the harbor just south of the city.

In fact, it was this very harbor that was of special attention today.

Not due to any grand event but due to a lone butterfly sitting on a lone dandelion, which grew from a crack in the concrete floor where the walls of a warehouse met the ground.

In another universe or timeline or whatever one would like to call it, the butterfly would have simply remained motionless.

Today however, for no particular reason, it flapped its wings.

The act, unfortunately, drew the attention of a small bird atop said warehouse, which swept down with practiced ease and caught the butterfly in its beak.

Not to far away one of the many harbor workers stopped in his tracks for a faint few seconds to look at the bird before it flew away once again.

With the bird gone, the worker returned to his duties and walked into the warehouse where he would get supplies destined to be transported to some expedition in the far south. Though first they had to be loaded onto the HMS Tempest, a cruiser currently docked at the harbor.

/ / / / / / / / / /

The Tempest left the harbor but moments later than in an other world and set a course to Earth's south pole.

For one, she was carrying supplies for an expedition underway in that icy wasteland but perhaps more importantly she was ferrying a single man there.

The Tempest's captain had his reservations about being reduced to a glorified taxi, yet he had been instructed by his superiors to not bother the man.

An order that came from the UN itself, for reasons he could only guess at.

Even the man's name was unknown to the captain, though the PDA he was so often seen with carried an engraving: "O.P.".

It wasn't that the man was unfriendly either; one could speak to him fine, however he treated all information about himself and whatever he was doing as if they were classified to the highest degree.

All thing considered, they likely were.

/ / / / / / / / / /

The Tempest and those aboard her were nearing their goal, it would only be another three days until they reached the site of the expedition. Well, technically they were only slightly more than two days away, however the Tempest couldn't go in a straight line to their destination, as she was busy avoiding the large slabs and mountains of ice floating around.

The sea and wind were calm, a slight breeze flowing over the ship as the sun set below the horizon, reflecting its last red rays of light on the mirror like water.

The calm, however, was not meant to last.

" Sir! We are getting radar returns! It- It is-, I don't know what it is." , a nameless technician overseeing the radar called out.

" Wake the captain! ", the ship's second in command ordered, " Declare battle stations".

"My God" the navigator muttered to no one in particular, as the sky turned from a matte black to a glowing crimson. The stars in the heavens soon blocked out by the unrelenting red light.

"Report!" the captain bellowed out as he entered the bridge.

"Sir!", the radar technician began again, "we are getting radar returns,

bearing R089"

"We lost all contact with command", the communications officer followed with his report.

Now it was the navigators turn to speak: "The GPS is down and the compass is useless as well"

Before any more reports could be given an other call echoed through the bridge: "We have visual contact!"

Turning to his left, the captains mouth was left agape, as titanic white wings stretched out into the sky.

The bridge crew stood in silence, oblivious to the door behind them swinging open.

"what is the meaning of this?" the nameless man asked in a stern voice while entering the bridge before he too began staring at out of the bridge's port window.

"No...", the he said in disbelief "they wouldn't have..."

"We are picking something up!" the comms officer began, "A distress beacon, from the expedition site!"

At that the captain had snapped out of his stupor and began taking charge again. "Do we have a targeting lock?"

"Affirmative, missiles ready"

"open fire"

A series of hatches opened on the cruisers stern. From them, missiles soared into the crimson sky before deploying their own wings and turning to cruise towards the white giant slowly rising on the horizon.

Soon the giant now stood fully erect, seemingly towering into the heavens themselves, before vanishing again in a white flash of light.

"BRACE!" someone screamed as a shock wave tore over the water, ending whatever calm once existed here for good and soon after hitting the Tempest. The gargantuan force shoving the ship aside, as it narrowly missed one of the many pieces of ice drifting in the water.

Had the Tempest been but a few seconds further ahead in its tracks, she would have collided with a force that would have ripped her bow clean off, undoubtedly sinking the ship.

But alas the Cruiser still swam on the quickly rising seas, her crew and the odd man having survived this fateful day instead of being cast to the ocean floor, as they were in an other world.

/ / / / / / / / / / - 15 Years Later - / / / / / / / / / /

Shinji sat unmoving in one of the seats in the employee lounge of the harbor's administrative building. His back was killing him, as were his arms and legs. And worst of all, it was already afternoon and he had none of his actual tasks finished, meaning to be done with his work by the end of the day, he'd now have to work double time. Either that or pulling an impromptu night shift.

Indeed it seemed the universe had decided to be cruel today. When Shinji woke up he had been prepared for an uneventful day at the harbor: change some burnt out light here, empty some trashcans there, perhaps sweep some halls in the many buildings in and around the harbor. But no. When he left his home, aka a large-ish utility closet he took over, he was greeted with the news that one of the many trucks at the harbor had an oil leak over night. OK, no big deal, get some sand and- turns out the truck was standing on the grass fields surrounding the harbor.

And thus, a young teen had spend the first half of a long day digging up nearly six cubic meters of contaminated dirt. His purple rubber boots still had small patches of dry earth sticking to them, while his purple uniform, denoting him as a member of the harbor's janitorial force, was completely soaked with sweat.

A look at the clock. '14:06, shit, time to get moving'. Shinji's body protested his attempt to go back to work, but it was either this or only four hours of sleep tonight.

A mechanical whir came from one of the offices connected to the break room. Deciding to check it out, even if only to avoid work a little longer, Shinji opened the door to said office. Namely that of the harbormaster. He identified the source of the noise to be a fax machine atop one of the many file cabinets lining the office walls. He stepped into the office, leaving a faint trail of dirty footprints behind. The office in question was currently vacant, as its usual inhabitant was outside overseeing the resupply of an aircraft carrier currently docked here. "Over The Rainbow" was its name if Shinji remembered correctly. The ship had docked this night, so he didn't have the chance to check it out yet.

Taking his attention back to the fax machine, Shinji found it was currently printing, or rather vomiting out a single piece of paper. There was something off about the loose sheet of white office paper sitting in the fax machine's tray. Usually when files came in they took an awful amount of time to print, as they were filled from top to bottom in fine text. And the fax machine wasn't young either.

But that wasn't the thing drawing his immediate attention. No, what was truly off about the fax was that it was addressed to Shinji himself.

It was already rare enough for him to get a regular letter and those were always from companies going through every possible name and address to send out advertisements. To think, however, that someone would go through all the trouble of sending him a fax was unbelievable.

Nevertheless, curiosity got the better of the boy as he made a final step towards the fax machine and grabbed the almost clear paper. It was addressed to him after all.

He didn't know what he had expected, but this was not it. Bewilderment overcame him as he stared at the nearly blank page and the few words printed on it.

To: Shinji Ikari

From: NERV, Central Branch

Re: You are needed.

Come. Immediately.

Signed: Gendo I.

For such a short letter, Shinji found, there was a lot to unpack here.

Firstly, he had just been ordered to Nerv central. While that did tend to happen here from time to time; he was working on a Nerv harbor after all, he never thought he'd one day get summoned. Usually these summons meant that you had messed up badly enough to earn the attention of the people who owned the place. Needless to say those summoned rarely returned.

Shinji, however, didn't think he ever messed up his job THAT much. But then again the way the fax was phrased didn't really indicate that he was in trouble. After all, it said that he was needed; something he hadn't heard in a long time.

Secondly, the fax was an odd mixture of formal and informal. It followed the basic layout of a letter, but the actual message only contained two words. He doubted that any self respecting company would send such a thing out through official channels without a very good reason.

All of these observations, however, paled in comparison to the third reason for Shinji's bewilderment; as thirdly: the fax was signed by his father.

Gendo. It was a name he had not heard for years on end at times. It was a name he never thought he'd hear again except in hushed conversations. It was a name he never wanted to hear again. Not after what happened to him.

Shinji could feel a vile mixture of rage, disgust and hatred boil inside him. His heart beating like a sledgehammer against the inside of his chest. After all these years, after all he had to go through, after all that has happened to him when he was abandoned by his own father, now the man had the gall to do nothing less than demand his estranged son come back to him for god knows what reason.

After all that's happened to him...

Shinji touched his lower back on the left side. Though he was fully clothed, he knew where the scar lied.

His hands began to tremble and his grip on the fax began to loosen. The boy recognized the feeling, it was like sitting on the beach and watching as all the water suddenly recedes. On the metaphorical horizon he could already see a tsunami of repressed memories barreling towards him with a force that would tear his mind apart and bury it in deafening fear as he would be forced to relive his childhood. It wouldn't be the first time this had happened.

He needed fresh air. Now.

Outside the harbors administrative building there was a flurry of activity. Much more than half an hour ago when Shinji entered the building to rest after digging quiet a sizable hole. People were working at break neck speeds, loading creates and boxes onto the hulking gray shape currently docked at the port. It must have easily been 300 meters long. It was big enough, that even from where he currently stood, a good kilometer away from the water, he could still make out the bold white letters on it's hull, even if only barely: "Over the Rainbow".

Among the various workers going about their duties faster than they should, there was military personnel talking to them and directing them.

As Shinji tried to make sense of what was going on all the sounds and smells of the harbor hit him. The loud and relentless whirring and beeping of machinery that he had learned long ago to tune out. His nose was telling him that there were chemicals in the air, alongside a faint note of gasoline, but that was also always the case. Perhaps his sense of sight could provide answers?

Looking around in the chaos of the harbor and ports, Shinji again failed to get any worthwhile information. It was afternoon after all, so the sun was illuminating the facilities and the light gray concrete ground, the light reflected of it in turn made seeing anything, except maybe the large aircraft carrier, rather difficult if one just came form indoors.

As his eyes adjusted to the light, Shinji finally stopped squinching them, something he hadn't noticed he was doing until he stopped. Being able to see clearly now, the teen was able to make out the familiar form of the harbormaster, who was talking to two men wearing green camouflage. The harbormaster pointed in his direction and the men began quickly walking towards him, closing the several dozen meters between themselves and Shinji in a mere handful of seconds.

"Shinji Ikari?", one asked. He was slightly taller than his companion, his voice wasn't exactly rough but it had definitely seen better days.

"Y- Yes?",the boy in question stammered. He wanted to know what was going on, why there was such a commotion, but with all the questions he had about his current situation and more importantly the fax, his mind struggled to put two words next to each other in a coherent manner. The heat wasn't helping in that regard either.

"We are under orders to escort you to the Over the Rainbow, from there you will board a plane to bring you to Tokyo-3.", the slightly smaller man spoke. His voice was smoother and he looked younger than his colleague.

If there was a mental equivalent of a blue screen, Shinji was experiencing it right now. Too many new things happening at once. He was completely ripped out of his beloved routine and was now apparently going to Tokyo-3, where he would likely meet...

"Do you understand?", the older one spoke.

Shinji did, in fact, not understand. There were simply too many questions that he wanted to have answered. Too many to even know where to begin asking.

A loud, sharp noise pierced the air. The young teen, finally snapping out of whatever trance he had been caught in, looked towards the source of the sound: two planes climbing into the sky. From the angle they were flying at, it was without a doubt that the aircraft carrier present had launched them.

The two men also looked towards the pair of planes before returning their gaze to the young teen, who still hadn't moved or given them any sort of acknowledgment.

"We are going.", The older one stated before the younger one grabbed Shinji by the wrist and began dragging him along as the three of them made their way towards the Over the Rainbow.

It was a hot day as the sun bore down upon the earth. There were many nice things one might do on such a day, like swimming or eating some ice cream.

Jogging in full janitorial attire through an overcrowded harbor was not among these things. Shinji still hadn't spoken, now though it was simply because his lungs were burning up inside of him. His wrist was still held in an iron grip but at least they seemed to come close to their goal.

The trio was maybe 100 meters away from the Over the Rainbow as another pair of planes was launched from the carrier and rose into the sky. The boy winced at the noise and to his surprise even the two soldiers flinched a bit. Still, they had to keep moving.

Reaching the flight deck of the super carrier was no easy feat, as one had to go through a seemingly endless labyrinth of utilitarian corridors to reach a staircase leading upwards all the way to the bridge of the ship. At least the two men knew their way around the place.

Stepping of the staircase at the half way point, Shinji found himself on the carriers main deck. It was a hub of activity; Planes were moved around, fueled and loaded with missiles and bombs. On the far side of the ship there was a lift currently bringing an other jet up to the flight deck. And between all of it, technicians were running around and tending to their various duties.

It was chaos. A chaos far greater that what he had witnessed in the harbor but minutes ago. Yet, it was also far more organized, as each person on the flight deck had a purpose that they fulfilled. Organized chaos, an oxymoron one might think, but Shinji was witnessing it this very moment.

Behind two fighters on the flight deck flaps rose up as most technicians quickly retreated from them. And then from one moment to the other, the planes were catapulted forwards, leaving the ship at incredible speeds before they began climbing into the air. With the planes gone, the carrier's crew swarmed the flight deck again to bring an other pair of planes into position to repeat the process.

Shinji, however, didn't get to watch the flight deck any longer as he was dragged towards a VTOL waiting next to the carrier's island. The Over the Rainbow was docked with its port side facing the harbor, as such the large tower that was the island on her flight deck blocked the view of the sea. A view which Shinji only got to see as he and his escort reached the VTOL.

While the two men talked to the VTOL's pilot, Shinji seized the opportunity to look at the sea.

In the distance, not quiet on the horizon, but still far away there were dozens of ships sitting on the glimmering water. There were no waves and the sky was clear save for a few clouds. The teen nevertheless felt like he stood in eye of a storm, as the calm and quiet he had enjoyed so much about living and working at the harbor was gone. Replaced with uncertainty and fear as he was dragged off to a far off city where he would presumably meet his father.

The thought made his stomach turn. Luckily, Shinji didn't have to keep his mind on such matters as now there were little specks of light rising from the ships in the distance. The lights were just barely visible against the bright blue sky, however the trail of white smoke in their wake indicated the lights to stem from rockets. This theory was further supported by more lights, more missiles, rising from the ships who were now half enveloped in white smoke. Shinji could only follow them only so far before the sun made the missiles impossible to see. Though they seemed to turn in the same direction as the planes.

"get in.", The pilot had now turned his attention to the adolescent who was currently staring at the sea, lost in thought. "Hey!", the pilot began again, this time grabbing the boy's shoulder and turned him around. The teen, evidently surprised, began to stutter out some amalgamation of an apology and confirmation: "Ah- y-yes, sorry, of course". Soon after Shinji found himself hurried into the VTOL's passenger compartment located in the aircraft's body. There the pilot properly strapped him into one of the seats.

With himself secured and the co-pilot, who had remained in the cockpit the entire time, doing pre-flight checkups, Shinji was finally given any sort of debriefing. "OK, listen up, Shinji! We are going to be flying you to Tokyo-3, OK?". It wasn't really a question, after all, Shinji was in the aircraft already. The pilot now kneeled to be on eye level with the sitting boy. It was a nice gesture and certainly helped to comfort the scared teen.

The next words spoken, though, washed away any comfort there might have been in Shinji's current situation. "But before we can get you to Tokyo-3, we have to fly an attack run. You see there is a big monster attacking Japan and we currently need all planes we have on the job. So we'll do that first and then drop you off when we refuel and rearm at Tokyo-3. But don't worry, the monster can't reach us while we are flying". The pilot conveniently omitted information that he felt would worry the boy any more that he already surely was.

Such as their attack run not being a strategic or tactical necessity, but rather the result of the admiral in charge of the carrier strike group being butthurt about being, as he called it, "reduced to ferrying a damned child around". Furthermore the pilot omitted that the monster they were about to engage had already torn through several tank battalions on its way to Tokyo-3. Its destination wasn't hard to figure out, considering it had been walking in a straight line since surfacing on Japan's east coast.

With everything the pilot had to say being said, he got up and entered the VTOL's cockpit. Once he had taken his seat, he too began working away on his consoles while the co-pilot was talking to the carrier's bridge. From his seat, Shinji could see and hear the entire act, though unsurprisingly he understood nothing.

Before he knew it, the VTOL was lifting off the carrier. Then, once clear of the deck, it began climbing while also beginning to head towards the direction he had seen the planes launched earlier turn.

Though they never climbed into the clouds, from his position in the VTOL's passenger compartment, one could still get a good view of the sky. It was filled with black and gray shapes dancing around. Some were coming towards them.

Before long the VTOL Shinji found himself in was no longer alone in the sky but surrounded by others of its type. All bearing UN insignia. Once enough had gathered, they headed off towards their target.

/ / / / / / / / / /

Shinji woke up from his short stress induced nap when the plane shook.

"just turbulence, but you still might want to hold onto something, we are almost there.", the co-pilot quickly provided. He must have noticed that the teen was shaken.

By now the afternoon was gone and it seemed the sunlight was approaching its final hours for the day. It was also cooler. When Shinji got into his seat, the sun was still bearing down with full force, though the inside the air conditioned aircraft was held at a comfortable temperature. Now Shinji actually shivered slightly from the cool air inside the VTOL.

Freezing. These days few had the luxury of experiencing the sensation. He himself had only truly frozen a handful of times, like when he had to clean the harbors cold storage, used for food and medicine. As such he would hold onto the feeling the cold produced when it graced his skin. Soon he would be working in the blazing sun again, that was certain.

Yet any further contemplation of the cold air had to be put on hold as the pilot spoke up: "We have arrived, hold on tight".

Shinji did just that, not daring to speak as the pilots began talking over the radio; filling the plane with military jargon. The VTOL leaned to the side and made its way around one of the many mountains in the region. And there... There...

The teen stared in awe and terror at the giant humanoid figure. Truth be told when he was told said they'd fight a giant monster he assumed the pilot somehow wanted to downplay the situation to calm him. But to think that they would fight a literal monster...

Explosions rang out across the vacant town below them, produced by a steady stream of missiles coming from the pods located under the VTOL's short wings. Missiles that all hit the greenish beast dead center but failed to produce any results for their efforts.

The giant simply strode forward, unbothered by the UN's and JSSDF's efforts to stop it. All the while the VTOLs maintained a steady distance around it, firing more missiles to no effect.

By now Shinji was frozen in his seat with terror. Soon, he kept telling himself, soon the missiles would run out and they could fly away.

However those who had their names written in the book of life could not abandon fate. And while Shinji's part in the play had begun long ago, now it was time for him to take a leading role.

The green giant stretched out its arm and pointed it at the VTOL in which Shinji currently sat. Even the two pilots tensed up and held their breaths as they tried to maneuver the aircraft away. But alas it was not meant to be.

A purple lance shot out from the titans hand and pierced the VTOL, cutting it apart. Shinji closed his eyes. He didn't want to die. He simply wanted to go back to his life, to his simple routine at the harbor. Was that too much to ask for? Was it too much to ask for a life in which he could forget his past and simply exist in peace?

His past... Perhaps death wasn't such a bad alternative either. After all, never having to remember his childhood was an enticing concept. So enticing in fact, he had often considered giving death a helping hand.

Though again, Shinji's musings were cut short as the seat he was strapped to came loose as what remained of the VTOL began falling. And when it finally hit the ground...

/ / / / / / / / / /

As Shinji began recovering from his dazed state, he found himself lying in the middle of an intersection. Behind him the VTOL's wreckage burned brightly. It seems he was ejected when the aircraft crashed. Quickly looking around, there were some payphones along a building wall, behind him was the burning wreck and further down the road was... a girl?

She had light blue hair and wore an unremarkable school uniform. She seemed to simply stand there and stare at him. As his eyes began adjusting and slowly he could make out more details. She definitely wore a school uniform and her eyes, they were... red.

A loud crash came from behind him as his sense of sound returned to him. The dazed teen shifted slightly, still lying on the street, to see what was going on. To his continued terror he found a large green foot had stepped onto the burning wreck, setting off any remaining fuel and ammunition.

Looking back to the girl, he wanted to scream at her to flee but it seemed she was already gone.

A screech tore through the air. Not that of a human or any animal but that of thoroughly abused brakes. He could make out a blue shape coming to a stop next to him. A car it seemed.

the passenger door swung open. "Quick, get in!", someone told him. By now his sense of touch had returned as well. Or rather his sense of self, as Shinji could feel his body again.

Pain. That word best described his current state. Every limb, every muscle, every organ, every bone and every fiber in his body was hurting. It was the kind of pain that was so absolute that it smothered any coherent thought.

Despite being ordered by someone to get into their car, presumably to flee, the best he was able to do was to get into a fetal position on the ground.

"Shit!", an other car door opened, "are you hurt?", someone was approaching him, "let me help you". There was an other crash behind him. It seemed the giant had decided to move on. Someone grabbed him and heaved him into the car's passenger seat, before his door was slammed shut.

Now the person got in the driver's seat, before closing their door as well. Finding the strength to overpower the pain, even if just by a bit, Shinji turned his head to look at his savior. He, or rather unmistakably She was a bit taller than him, wearing a black dress and sunglasses of the same color. Though her most striking feature must have been hep purple hair.

"So", the woman floored the gas pedal "I'm Misato, who are you?"

End of chapter 1 -

Author's note:

Holy hell, writing stuff takes a long time. Nevertheless I have an idea for a full fan fiction and I intend see it through ( yeah, I know, famous last words before the story gets abandoned half way through).

Though with that being said, there will be new characters and a new organization that opposes NERV and SEELE on a fundamental level.

I should also add that this series will not be of the "slow burn mystery" kind; I intend to get Shinji's revamped past out of the way by the time Asuka comes around so we can get to the actual conflicts. This means that after the fight with Ramiel will be where the story truly begins deviating from the original.

With all that out of the way: criticism is always welcome, have a good day.