DISCLAIMER: This is a work of fan fiction incorporating characters and situations from the Gainax manga/anime series Neon Genesis Evangelion and its related feature film releases. Gainax and its various media distributors hold sole exclusive rights to their use. The author is in no way affiliated with Gainax or its distributors, nor has this story been submitted for any commercial purpose.

by Ikarus Onesun

Chapter One: The Second Option

Maya Ibuki's hands flew frantically over the keyboard at her station, trying every possible combination of parameters she could think of, to no effect. Loud warning signals blared in the NERV command center and blossomed angrily across the main projection screen as Dr. Ritsuko Akagi and Major Misato Katsuragi looked on, the crimson glare from the flashing warnings accentuating the concern clearly showing on their features.

"It's no good!" Ibuki shouted over the din of the warnings. "His ego border is in a fixed loop!"

Ritsuko strode over to Ibuki's station, glanced at the data scrolling rapidly across her subordinate's terminal, and frowned.

Damn it! she thought. Just like the last time...

"Try to radiate the wave patterns from all directions," she suggested, her voice heavy with tension. Ibuki quickly punched in the necessary formulae and sent the command to the MAGI to process. Instantly, another sequence of warning messages flashed across the screen. Ibuki's eyes quickly scanned the new data from the entry plug, then glanced up at Ritsuko, a look of hopelessness spreading across her face.

"No," Ritsuko muttered darkly, "the radiated signals are captured in Klein space."

Misato's head snapped up. She had no idea what Ritsuko was talking about, but the doctor's tone did not sound encouraging. "What... what does that mean?" she asked breathlessly, as she clutched at the cross pendant around her neck.

Ritsuko turned to her, her face taut, her green eyes downcast.

"It means... we've failed."

Misato paled. "W... what?" she stammered, unable to believe her ears.

The doctor turned her head slightly, and said to Ibuki, "Stop the interference. Reverse the tangent graph. Set the addition value to zero."

"Yes, ma'am," Ibuki complied. Her fingers flashed away at her keyboard, and immediately the warning messages on the main screen disappeared.

"Aoba?" Ritsuko said to the long-haired technician seated opposite Ibuki.

"Nothing," Shigeru Aoba responded, his eyes scanning the graphs projected before him, "No destrudo reaction detected. Pattern is white. The ego formation in the LCL has... completely dissipated."

Ritsuko nodded, turning back to Misato. The look of utter defeat on the doctor's face said everything to Misato before Ritsuko could even utter a word, and the major shook her head rapidly as Ritsuko told her what she had hoped and prayed she would not have to hear.

No, she thought, oh, God… please, no…

"Misato... Misato, I'm so sorry... we did everything we could..." Ritsuko murmured.

Misato looked back at the doctor blankly, disbelief and despair warring across her features. For long moments, she just stared silently at Ritsuko, forcing the doctor to eventually look away uncomfortably. Several minutes passed, during which one could have heard a pin drop in the command center. Finally, Misato turned to the bay window overlooking the EVA cages, and rage suddenly flared in her chestnut eyes as she fixed her gaze upon the silent form of Evangelion Unit 01, berthed in its cage and secured with heavy shoulder restraints. With a keening wail, Misato grabbed a stack of heavy manuals from the desk beside her and flung them at the shatter-resistant glass, the books bouncing off harmlessly. Grief and fury possessed her as she pulled a wheeled chair out from under the desk and, with surprising strength, heaved it toward the window as well, the onlookers on the bridge flinching as it clattered off the pane and skidded across the floor. Finally, Misato ran to the window and began beating her fists against the glass, all of the frustration, anger, and fear that had built within her heart over the past thirty-one days suddenly bursting from her as she screamed at the impassive mecha on the other side of the glass.

"What good is science if it can't save one person?" she lamented, hot tears streaming from her eyes as she pounded the glass and shrieked at the EVA, "Give me back my Shinji! GIVE HIM BACK!"

Misato's strength suddenly failed, and she sank to her knees, sliding down the glass pane as Ritsuko rushed over to her. Not knowing what else to do, the doctor embraced her friend from behind and gently eased her down as Misato collapsed in her arms, her body shaking in the grip of her mournful sobs as they slid to the floor together.

"...give him back," she whimpered, over and over, "…please... give him back… give me back my Shinji..."

Ritsuko could not think of anything to say, too saddened and stunned to possibly express any words of comfort to her. All she could think to do was to simply hold her grieving friend, who clung to her as if she were drowning. The two women knelt on the floor of the command center clutching each other, Misato's sobs the only sound that broke the deathly silence that had descended over the bridge.

They had failed. After thirty-one days, after all of their efforts, Shinji Ikari remained trapped within Evangelion Unit 01, and everyone present in the command center at that moment shared in the same, terrible fear – that the young pilot was now hopelessly, irretrievably lost.

o o o

Much later, after a dazed, distraught Misato had been taken home by a Section Two agent, Ritsuko had dismissed the bridge crew, made herself a very large pot of coffee, and sat at her desk to begin analyzing the data from the failed attempt to reconstitute Shinji's body within the entry plug. She had only one other past scenario to compare that day's results to, and so far, her numbers all looked depressingly similar to the data NERV – or GEHIRN, as it was known at the time – had collected from the one previous attempt to recover the body of a pilot who had been absorbed into an Evangelion.

After ten years, they still had not found a solution to the problem – and they had still not managed to find one after today.

This could complicate things enormously, she mused, sipping from her coffee mug as her green eyes flitted across the data on her screen. If Shinji's consciousness can't be recovered from within Unit 01, there's a high probability that it will not be able to accept another pilot - and after this latest incident, we can be reasonably sure that it won't accept the dummy system either…

There has to be something else we can do... but what?

She pulled open the bottom drawer of her desk, reaching in for the ever-present carton of cigarettes, and was extremely annoyed to find it empty.

Kaji. Goddamn it, she fumed.

That's four packs the sonofabitch owes me now...

Ritsuko crumpled the empty box angrily and pitched it into a nearby garbage bin in disgust. She leaned forward and rested her elbows on her desk, letting out a frustrated sigh as she closed her eyes and wearily rubbed her temples.

As she sat in silence, wracking her brain for anything, anything at all that might be tried, and coming up with nothing again and again, her cellphone rang. She picked it up absently and touched the TALK button without bothering to check the number.

"This is me."

Commander Gendo Ikari never identified himself by name on the telephone, at least not to his subordinates. There was no need. The man's cold, emotionless tone instantly identified him to anyone on the other end of the line.

Ritsuko braced herself, for the ice in the Commander's voice was a clear indication as to the direction this conversation was sure to take.

"Yes, Commander," she replied, "The operation was... unsuccessful."

"I am well aware of that fact, doctor. Today's outcome was... disappointing. Nevertheless, a solution must be found, and quickly. We cannot afford to have Unit 01 out of action for an extended period. Our time is growing short."

Does he even care that his own SON is still trapped inside that thing? Ritsuko wondered.

At least we seem to have reached the same conclusions about the viability of a replacement pilot, and of the dummy plug…

"Yes, sir. I apologize. I am going over today's data right now, and while I can't say for certain until the MAGI complete their full analysis, my first impression is that Shi... that the Third Child's ego pattern is simply not strong enough to reconstitute its physical form on its own. We couldn't even previously manage to achieve this with a mature ego pattern, so his case would seem to be even more difficult. I'm trying to think of ways that we could somehow augment his wave pattern externally with the MAGI's help, but nothing immediately comes to mind."

Ritsuko took a deep breath, and decided to take a risk. "If you're free, perhaps we could order something to eat, and go over the data together? The two of us might be able to come up with a possible…"

Ikari abruptly cut her off. "I want the entry plug removed from Unit 01, sealed with its contents intact, and taken to Central Dogma immediately. If the plug eject signal continues to be rejected by the unit, have the technicians remove the plug manually. We will use the second option, just as was previously done. This project is to be undertaken in the strictest of confidence, do you understand me, Doctor?"

A stunned Ritsuko said nothing for long moments. Ikari's tone darkened as his voice crackled on the line. "Do you have a problem with this?" he snapped.

"Sir... the second option... it… it didn't work last time – at least, not in the manner in which it was intended," she stammered, unable to believe that the Commander was even considering this.

"Irrelevant. You said before that the Third Child's pattern was not strong enough to reconstitute his body on its own. If that is the case, then the only reasonable alternative is to provide a viable surrogate vessel for his pattern to inhabit. You certainly know how to accomplish that particular task, do you not, Doctor Akagi?" The Commander's voice dripped with condescension, as if he were speaking to an uneducated field worker, rather than a Summa Cum Laude PhD graduate.

Ritsuko bit back her indignation. "But sir... there is still the problem of how to extract the wave pattern from the EVA! Creating the… vessel was not the primary difficulty in the first attempt..."

Ikari's response was immediate. "The current process will be sufficient once the vessel is re-introduced into the active environment. The previous attempt encountered its own specific… difficulties, none of which will apply in this situation. The difficulty in this case will lie in breaking the unusually strong synchronization between the subject's ego pattern and the EVA in order to separate the two, which will have to be done forcibly. A powerful electromagnetic surge through the EVA's core should disrupt the sync ratio long enough to allow the MAGI to isolate the Third Child's pattern, and once it has been given an obvious avenue for transference, it should not be difficult to subsequently extract it from the core and reincorporate it into its surrogate form. I am confident that the MAGI will validate this hypothesis, and will predict an adequate margin of success for the operation."

He sounds like he's describing mundane probability theories and textbook bioengineering concepts, but this is Shinji – his own son – he's talking about experimenting on, Ritsuko thought.

I thought my mother could be a cold hard bitch sometimes, but this man...

"I... understand, Commander," she murmured finally. "You do realize that, just as before, this… surrogate vessel will not be an exact copy, due to the current physical state of the genetic material? We still won't be able to isolate a pristine sample, and there will certainly be some… unpredictable side effects as a result, although we do now have some idea of how they may be manifested. These could potentially cause significant psychological damage to the subject's psyche, assuming that the recombination process will even have a successful result."

Ikari replied shortly, in a tone that could cut glass. "As long as the result can still pilot, these concerns are irrelevant, Doctor."

Ritsuko's jaw dropped at the pure callousness of the Commander's remark.

Ikari continued. "Have the entry plug sent to Central Dogma immediately. I want the vessel prepared and ready within seven days. In the meantime, all work on the dummy system is to be suspended until this project is completed, and Central Dogma is to be deemed off-limits to all non-essential personnel – including Rei."

The sneer on the lips of the Commander was almost audible to Ritsuko over the cellphone. "Do not fail me again, Doctor Akagi."

With that, the line abruptly went dead.

Bastard, Ritsuko thought, clicking her phone's END button and slamming it down on the desk.

She reclined back in her chair, sighing heavily, as her thoughts eventually shifted from her unpleasant conversation with the Commander to the project she had now been ordered to carry out. She contemplated the various theorems that they had discussed, her train of thought flying at an incredible pace as her brilliant mind leapt between concepts, connecting each one in turn until she eventually came to the inevitable conclusion.

It could work, she grudgingly admitted to herself, after pondering the problem for long minutes.

He's right.

I HATE it when he's right…

Though at times it was a hard pill for her to swallow, the Commander's intellect was as sharp as her own – possibly even sharper. Perhaps this was the reason for her strange attraction to the cold, distant man – he was really the only person she had ever met, besides her mother, who was her intellectual equal, and this was a characteristic that she found extremely appealing. She had been with a few men in her time – though certainly not as many as Misato – but things never managed to progress beyond a few dates and the occasional half-hearted sexual tryst. Ritsuko desired someone that could relate to her at her level, who could hold his own in a relationship with someone of her vast intelligence and breadth of knowledge – and Gendo Ikari was certainly more than a match for her in that regard.

Once Ritsuko and Ikari had begun working together after her mother's death, they had spent many evenings having the most fascinating conversations about biotechnology, about the recent breakthroughs in organic-based superconductivity and how these findings would one day be applied to the EVAs, and eventually, once she had gained his academic respect and trust, he had revealed to her the secrets of the Human Instrumentality Project – and she had been spellbound by its possibilities.

She had been thrilled that Ikari had deemed her worthy of participating in such an vastly important endeavour, and she had expressed her gratitude to him both publicly – and privately.

Ritsuko truly believed that she had found in Gendo Ikari the closest thing to a soulmate she had ever encountered. She was intoxicated by the depth of his intellect and the scope of his vision, and had been completely swept away by him.

However, he was not always the easiest person to deal with – as their earlier conversation had plainly demonstrated. Superior officer or not, it was her infatuation with his incredible intellect that caused her to put up with his abrupt, callous demeanour. She would never tolerate such treatment from anyone else.

She had never met Yui Ikari, but Ritsuko imagined that Shinji must have inherited much of his mild, gentle manner from her.

I've never seen a father and son so radically different from each other, she mused.

Shinji did bear a strong physical resemblance to his father – give him a beard and glasses, and he'd be the Commander in miniature, she thought with some amusement – but on the inside, they were as different as night and day.

And in a week's time, who could say what Shinji Ikari would be like – if they were even able to bring him back at all?

He'll never be the same afterward, that's almost a certainty, she thought.

But at least he'll be free of the EVA.

She frowned, recalling the Commander's shocking lack of concern about the dangers of possible side effects to his only child.

Once he realizes what we've done, I doubt that he'll thank us, though.

Ritsuko's fingertips chattered away at her computer keyboard as she called up all available data on what Commander Ikari had referred to as the "second option." The reports, from the old GEHIRN archive, were highly classified, and she was one of only three people in all of NERV who had access to them – the others being the Commander and the Sub-Commander. She paused long enough to help herself to another mug of coffee (it was clearly going to be a long night), and began digesting the contents of the various reports on the "second option" and the eventual result of that flawed experiment.

In terms of the stated aim of the project – the recovery of the lost pilot from the EVA – it had not been a success, yet they had still been able to make some use of the result nonetheless. In fact, according to Sub-Commander Fuyutsuki's own project notes, Ikari had not even seemed overly displeased by the project's failure, as if he had foreseen all possible outcomes of the experiment, and was somehow satisfied with this particular one.

This seemed very strange to Ritsuko, as it must also have to Fuyutsuki, as he had made a specific note of Ikari's reaction to the project's result. They both assumed that the Commander must have desperately wanted the original aim of the project to succeed.

Instead, it had failed, and the recovery of the pilot was not achieved – but incredibly, the result was somehow still acceptable to Gendo Ikari, a man who normally had no tolerance whatsoever for failure.

Was the outcome of the second option your true intention all along, Commander? Ritsuko thought uneasily.

And are you now planning to use your son the same way?


o o o

Author's notes: The idea for this story has been knocking around in my head for awhile now, and the germ of it can be found in a single line of Ritsuko's from Episode 20 of the anime. This line, combined with some insights that I picked up on from reading the RCB, led me to some conclusions about the origins of a certain character, and once I had that, I went on to think about how those same conclusions might be applied to a situation involving a certain other character. I might be way off base with my reasoning, but I decided to man up and run with the idea anyway. At the very least, it's shaping up to be a fun write, and I hope it turns out to be a fun read for all of you as well.

Many thanks to lachryiadhron for pointing out some construction improvements and for confirming some issues I had with scene settings.

Please feel free to leave a review, or drop me a line at ikarusonesun-at-gmail-dot-com.