As Evangelion Unit-01 tore a path of destruction through Tokyo-3 to the beach, the myriad wheels that constituted the mind of Gendo Ikari were spinning and spinning fast. People might fear him, people might hate him, and some misguided fools might try to use him, but all had to admit in the end that the man could think fast on his feet and had a talent for turning a bad situation into something that at least resembled victory.

Ignoring the strangled noises of terror escaping his second in command, he raised his voice so the others could hear him over the wailing alarms and panicked cries of his underlings to restore order to his kingdom. Contrary to popular belief, he was not immune to fear or panic, but he held himself to a level of control that made Buddhist monks look like decadent partygoers who exulted in excess. But he was still human, and sometimes he was more shocked than normal, and let the mask slip.

"Dr. Akagi, initiate the Gomorrah Protocol, and then target the entrance to the bay with whatever is left of the self-defense missile systems and empty the stores. Drive the Angel to shore, and deny it escape to deeper waters. Unit-00 is outfitted with the E-Type equipment, but Unit-01 is not. It cannot operate underwater. Attempt to contact both Pilots and inform them of the missile strikes. Once Gomorrah activates, reestablish sensor capabilities on the surface as soon as possible, and ensure there are at least two umbilical cables available for use." Though he spoke loudly, there was not even a hint of emotional tremor in his tone.

Dr. Akagi hesitated, staring up at the imposing figure standing atop his tower like a preacher from a pulpit, preaching fire and brimstone. "The Gomorrah Protocol? Are-"

Gendo interrupted her, saying "The Gomorrah Protocol, Dr. Akagi. Now." He was in no mood, now more than normal, especially with the current circumstances, to tolerate people not doing what they were supposed to. Which was, of course, doing whatever it was he told them to.

"Yes Sir." She turned to the technician next to her and began relaying the instructions as others attempted to raise the pilots.

Kozo turned to Gendo, who didn't give him a chance to voice his worries or questions. "We need to give him some room to play in, and I don't want SEELE finding out about this. Gomorrah will buy us some time at least, and we can blame it on the Angel. It's already shown abilities here that it didn't in the first battle, and the fact this battle is happening at all is a deviation from the norm."

The graying sub-commander turned to watch the main screen again, his face filled with worry. "At least we know with certainty how he'll react at Impact. The Demon has awakened, at last. Your updated plan has worked, at least as far as that's concerned.

Gendo shook his head as he sat down, ignoring the hustle and bustle occurring below them as they carried out his orders. "No, the Beast hasn't awoken. This is just the Berserker, and it's still just waking up. This isn't sustainable, not yet. Without an enemy on which to slate his rage and blood-thirst, he will lose steam and grind to a halt. We need a way to get him to the Angel. The missiles should keep it close to shore, but it's no guarantee of it getting within arms reach of Unit-01." He watched as an overlay on the main screen announced the activation of the Gomorrah Protocol, and then as one, all of the screens went dark as the external sensors went offline. "Things are moving faster than they should with both of them. I don't need displays like this occurring every time an Angel attacks." His frown deepened as he settled by habit into his normal position of slightly leaning forward against the table with his fingers steepled in front of his face. "Also, send someone to find the men who were supposed to take him into protective custody. How does a crippled and drugged boy just coming out of a coma get all the way to the cages and into an Evangelion?"

Despite the terrible grimness of the situation, Kozo had to laugh at the statement's absurdity. "He's your son, Gendo." he pointed out with a dark chuckle. "Would you let something like the fact you are merely missing a leg keep you from rescuing the woman you love? You're always telling me how the boy is like you. We probably should have expected something like this."

A small grin, unseen to all, flashed in and out of existence on his face as the base shook again as the missiles that made up the Gomorrah Protocol began to launch. "Perhaps. But then, it means we must ensure he does not find out about the particulars of the scenario. He's gotten quite good at shooting, and if he finds out what we are about, I doubt that he would miss me."

Eins, Zwei, Drei, Vier!

Asuka watched Dr. Akagi as she hurried about, shouting orders and typing commands into one of the MAGI terminals herself. While she was extremely curious about what constituted the Gomorrah Protocol, and why her Sempai didn't want to use it, she knew now was not the time to make a nuisance of herself by getting in the way. With the Prototype Evangelion lost under the waves, tethered to the massive Angel, and the Test Evangelion apparently on a rampage up above, the situation was dire, since she would be unable to take her Unit-02 up to resolve this mess as currently the leg wasn't anywhere near strong enough to support the weight of the massive giant.

So as she watched the hustle and bustle of the frantic techs as some tried to make contact with the pilots, her eyes caught the still form of the Commander. He was sitting now that he had issued his orders, and he looked as if he was unmoved by the situation.

He was so unlike his son! That whining, wailing, and otherwise unimpressive boy. It seemed strange and unlikely they could be related. She was sure that if the Commander had been present in the Entry Plug with her on the ship, they wouldn't have lost a limb to the Angel. And if they had, she was sure he wouldn't have thrown up in her hair. She giggled softly to herself, clamping a hand over her mouth to hide the sound as the thoroughly ridiculous mental image of the man standing on the ship's deck, his arms crossed and glaring the Angel into submission. But why had he picked his son to be a pilot, even if he was just the pilot of the Test-Type? He didn't seem to be the sort of man to allow nepotism. However, the way the boy was acting now was at complete odds with the frightened whining child he had been when they first met.

Why was he roused to battle now? Was it for the same reason why that girl had sequestered herself in his hospital room? She frowned as new, unwholesome, and unwanted thoughts formed.Are they an item? That's disgusting! No wonder they had ordered her out of the room; she had probably been doing perverted things with him while he was asleep! Of course, she mused, the only person that boring little boy could possibly make it with is a boring little girl.

Her eyes turned back to the screens, trying to unravel the mess of data screaming across the displays, almost too fast to track. Contradictory values flashed erratically on the screens, and her level of confusion only grew as she stared hopelessly at them as the base once again shook, the screens now briefly showing the words 'Gomorrah Protocol' before going dark.

Seeing that Dr. Akagi had come to a rest near her, Asuka caught her attention. "Sempai, what's the Gomorrah Protocol?"

Dr. Akagi sighed, shooting a dark look up to the tower and put a cigarette in her mouth before answering the girl. "It's part of our last-ditch defense plan. Gomorrah refers to our EMP missiles. We're going to detonate them over and around Tokyo-3 in order to try to disrupt the Angel's AT-Field. It's part of our last-ditch arsenal for a reason, though, because it will leave us blind and unable to communicate with the Evangelions, as well as disrupting their AT-Fields. We do have EMP proofed sensors in place, but not enough to suit me. There's also a window in which they shut down before Gomorrah initiates and then start back up after the detonation of the warheads, so it's still not a perfect solution." She rolled the cigarette around in her mouth. "In fact, it's not much of a solution at all. Wireless communications will be disrupted for a considerable time, and that's the primary way we communicate with the Evangelions."

Asuka thought about that for a minute. "So, what about Sodom? Is there a Sodom Protocol?"

"That's highly classified, Asuka. Sodom is not supposed to exist." The doctor looked around as Asuka pouted slightly, before bending down close to the redhead's ear. "Sodom is where we launch missiles with salvaged fusion warheads."

Asuka recoiled, horror dawning on her face as the doctor continued. "That's why it's classified. The Angels must be defeated at all costs, Asuka. I'm trusting you not to discuss this with anyone. I think you can be trusted with this, yes? I think you're more mature than the other pilots."

Pride blossomed inside the girl's bosom, as she beamed with all the brightness of the Angel's energy weapon, nodding vigorously. "Of course I can be trusted with this, Sempai! I won't let you down!"

What Dr. Akagi had not told the girl was that the enemies the Sodom and Gomorrah Protocols were designed to counter and defeat were not Angelic ones, but terrestrial foes. As terrible as these two options might be, they were nothing but pale shadows compared to the Revelations Protocol, which constituted the Commander's scorched earth option. There was no way she would discuss that with the girl, no matter how bright and eager she was. Not yet, anyway.

"External Sensors coming back online! Weapons systems reactivating!" The mousy tech shouted out as the main screen flickered back to life, showing the stormy beachfront. "Missile systems are back online!"

Ritsuko reached over the tech to put a key into a small, almost unnoticeable lock on the terminal and twisted it. "Tell them to launch everything we've got left in the stores," she said, straightening back up as the tech typed away into the computer.

Asuka frowned as the main display cycled through different cameras, trying to locate the Angel and the Evangelions, but all the available cameras showed was an empty beach and raging seas. Her eyes narrowed as the others watching began to voice the question burning in her mind. Where did that idiot go?

Eins, Zwei, Drei, Vier!

Under the waves, tethered to the Angel by the very tools she had hoped to destroy it with, Rei tried to ignore the inhuman screams of the Angel and the just as horrific roars of Unit-01. She looked at the display, trying to think and take stock of her assets and options. The arm that had broken under the stress of firing the modified harpoon gun had already healed, so she had use of both arms. The harpoon lodged in Unit-00's gut was going to be an issue, but she would not be able to remove it without making the injury worse. There was a limit to how much the system could self-repair, after all. There was a sudden jerking sensation as the power cable was ripped from Unit-00, and the five-minute counter appeared in the corner of one eye. Her jaw set and anger burning in her eyes, she set to work. This Angel had taken Ikari's leg due to the inadequacies of Pilot Sohryu, and she needed to balance that equation. While any actions of clean mathematical retribution against the pilot would most likely be frowned upon, she was free to take exponential vengeance against the Angel.

She twisted around to grab ahold of the cables binding her to the Angel. Engaging the turbines attached to her legs, she crawled her way along the cables to the Angel's side as it tried to shake her off.

Grabbing ahold of one harpoon, she punched her other hand deep into the white flesh, her AT-Field helping her to penetrate the Angel's side. Grasping onto a bone, she braced herself and twisted the fist inside of the Angel, causing the keening wail to intensify to ear-splitting levels. A look of satisfaction spread across her features, but she was not finished. With a tight grin, she ripped her fist out, bringing the broken bone with it. Reversing her grip, she applied Shinji's favored tactic of using the Angel's own body parts against them. It had been a winning strategy so far. She stabbed down with the sharp point of the bone over and over, carving out chunks of flesh as she tried to dig her way to the core. When the bone finally broke, she punched her fist back into the Angel, in an attempt to acquire a new weapon.

Gaghiel was not going to take this abuse without a response, however. Twisting around, it sped towards the surface, leaping out impossibly high, turning to come splashing down atop its attacker. Rei gasped in shock as the arm broke again as she lost her hold on the harpoon, causing her to bounce against the Angel's flank. White flesh bubbled around her, regenerating and healing even as the angel expelled her from it, and it swam off into the dark waters to spin back around, opening its toothy maw wide as it made ready to swallow her.

Not being the most graceful of things on dry land, to say nothing of being underwater, if Rei tried to swim away using the Evangelion itself, she would have failed. The massive cyborg was far from being buoyant because while it resembled the human form, the comparative densities were extremely off, and the cybernetic implants and armor weighed it down immensely. The E-Type equipment, however, was made to not only allow the Evangelion to operate better underwater, but to act as the primary movement system as well. Knowing her time was short, she kicked the larger propeller screws mounted to the back of her Evangelion's shoulders into gear and shot directly towards the oncoming Angel, locking her good arm into a spear, focusing her AT-Field around it for reinforcement. If she was fast enough, she reasoned that she could hit the core sitting in the back of the Angel's mouth with full force before it could bite down on her.

The kinetic force of several tons of Evangelion moving at high speed, smashing into the red orb, would probably be enough to shatter it if the core was of similar strength as the previous Angels. To be certain, the one that had caused them the most work in actually destroying it (other than this one) was the Angel Ramiel, as it had its core at the center of its armored shell. But even if the attack failed, she was not worried. Either it would work, and she died when/if it exploded (or she was rescued by the search teams and salvage craft, which she deemed unlikely), or she would die in the attempt. Either way, she would see Ikari once more, in this iteration or the next one. As far as she was concerned, it was a good plan, and it probably would have worked.

The flock of missiles slamming down into the water did exactly what they were supposed to do; disrupt, damage, and destroy. Shock waves slammed into both combatants, sending them off course and bouncing them around in the water, in addition to peppering them with shrapnel and heat. Angry tears mixed unnoticed with LCL as the plug finally went dark, and the last thing Rei saw was the orange blossom of an underwater fireball smashing into her as the power went out.

Alone in the gray, featureless tube, locked into place by the seat's restraints, Rei looked up to the top of the plug as the Evangelion began to sink slowly, still buffeted by explosions.

How long will it take me to die? she wondered, beginning to run the numbers through her mind. Hypothesis: With an undamaged Evangelion, the maximum rated depth with E-Type Equipment Load Out Alpha is one kilometer. The Bay of Tokai is five hundred meters at its deepest point. With the current estimated amount of damage to the Evangelion...

Eins, Zwei, Drei, Vier!

The vengeful giant strode through the water up to its waist, unable to go further in. He screamed his frustrations into the wind again, as the sky overhead burst into flame. The glaring visage of Unit-01 turned to the sky as the specially designed warheads detonated, causing massive pulses of electromagnetic waves to spread out, disrupting and destroying the electrical circuits over a wide area over Tokyo-3 and the surrounding countryside. Anything not shielded to be proof against such interference was fried, and the entire area over Tokyo-3 went dark. Even in space, spy satellites became multi-million dollar piles of junk as the orbital missiles detonated and the fluctuating magnetic fields played havoc with their circuitry.

The Evangelions, like the Angels so far encountered, were not effected by the EMP weaponry outside their communications suite, Dr. Akagi's explanation to Asuka being a complete fallacy in order to explain the existence of the emergency protocols.

Bored with the irrelevant light show, Unit-01 growled as it turned back to the shore, picking up one of the harpoons in its massive hand and turning back to scream again at the raging sea.

It was rewarded when Gaghiel and Unit-00 surfaced above the waves, locked in combat and ignoring everything but each other. It waded back into the sea, bellowing its challenge to the Angel, and screamed in rage as the blue Evangelion was taken back under. Unit-01 roared in frustration and hatred, its anger at being ignored, fanning the flames of its rage even higher.

'Look at Me!' it seemed to say as it screamed inarticulately, as it slammed its arms and fists down into the water, straining its legs to move forward. 'Don't you ignore Me!' the thing seemed to bellow, rage burning in the elongated diamond eye-slots of its helmet. It was all hot rage, anger, and hate, burning for the attention of its foe as the boy who sat upon the Throne of the Soul inside the Entry Plug screamed for recognition from the one called his Father.

But hate was not the only thing that drove this weapon, the God created by Man in the image of Man, for there was also love in the heart of the boy. As numerous members of the original Project E had pointed out, long ago in the early stages of planning when NERV was still only in the minds of Ikari and Fuyutsuki, people (and many, many animals) would do terribly bloody and violent things in the name of those they loved.

Shinji Ikari, a young man, a high school student, and Evangelion Pilot, might not know he loved one Rei Ayanami, a young woman, a (mad) scientist, and Evangelion Pilot, but the Berserker did. And the Berserker was not about to be stopped by a mere issue of physics.

If the water was what was keeping it from the fight, then the water needed to go.

Eins, Zwei, Drei, Vier!

Rei and Shinji were lying in bed together, nestled up close, legs intertwined, and his arms wrapped around her waist. Pale moonlight drifted in through his room's window, playing over their naked forms, showing the crumpled sheets and discarded clothing in piles on the floor. There was no sound but the sounds of them breathing and the beating of their hearts. She squirmed around in his grasp, turning so she could look into his eyes, and she ran her fingers through his hair. "I am cold, Ikari. Please keep me warm."

Squeezing her tightly to him, he nodded. "Maybe I should get more blankets."

"Perhaps. But I do not want to let go." She inched her way up towards his face, the warmth of his breath tickling her slightly. It is not... unpleasant. Hypothesis: His lips applied to mine will increase my body temperature, due to a chemical reaction and physical arousal. The emotional state of love, or intense physical attraction and desire. She closed her eyes as she moved to close in the last few inches, aware that numerous case studies suggested this course of action when about to engage in a kiss when something cold and wet hit her face. Confused, she opened one eye and saw tears running down his face. Why is he crying? There is no need to be sad. No need for tears. Perhaps it is like with the fifth Angel? He was crying when he opened the Entry Plug.

He spoke again, his voice frantic and oddly pitched. "Hurry, get that stretcher over here!"

She frowned slightly. I do not want him to be saying things like this before I loose conciseness. I wanted to think about kissing him.

She opened her eyes, the simple task seemingly impossible, to stare into the worried face of a man in a black rain jacket, trying to put an oxygen mask over her mouth. She tried to struggle but found there was no energy at all in her limbs. Relaxing, her head rolling to one side, a blasted landscape met her eyes, burning wreckage and debris everywhere, the dancing flames giving everything a hellish cast to it. The rain continued to fall, although the lightning had ceased.

"Ikari" she breathed, trying to find the boy's Evangelion, but she could not from her current vantage point, and it was too hard to move. She could neither grasp why she felt so tired nor explain the dull pain she felt throughout her body.

The man said something else to her, obviously trying to keep her awake. Of course. They are afraid if I fall asleep that I will go into a coma. But why are they so worried about me? It is Ikari they need to worry about. I wish he hadn't interrupted my dream. It would have been a pleasant last thought...

Rei closed her eyes as blackness overtook her, still wishing that her last thoughts would have been of Ikari's kiss.

Eins, Zwei, Drei, Vier!

Rei opened her eyes to a familiar ceiling, complete with its cracked tile. She sat up, looking around, oddly disappointed to find there was no one present. It would have been pleasant to find Ikari there, hopefully sleeping.

He always looks so nice when he is sleeping, she thought absently as she checked herself for injuries, pleased to note the absence of slings or casts. There was only a residual soreness present in her body, and she was still very tired, despite having just woken up from an indeterminate amount of sleep.

He probably did not escape the battle unharmed. There was a large amount of wreckage in the surrounding area, which suggests the Angel's core had detonated, either on its own or through external means. In addition, he had already been in a state that would normally ensure they would keep him in his own room.

It is strange they would have allowed him to pilot, given his medical status. The timing was extremely fortuitous, but I do not understand how they managed to get him suited up and launched in time once it was apparent I was being dragged underwater. Also, his appearance on the battlefield was heralded by the screams of the Evangelion. It does not scream, except during the bouts of extremely high synchronization with Ikari, what she calls the 'Berserker Mode'. Does this mean he once again managed an infinite sync score? Perhaps Pilot Sohryu was unable to synchronize with Unit-01, despite her reported boasts of being the 'best' pilot. If that is the case, then they would have had no choice but to place him into the Evangelion.

The smallest of frowns made an appearance on her features, looking out of place on her normally placid expression. I have failed the Commander again. I failed during the activation test with Unit-00, was unable to be sortied in the fights with the Third and Fourth Angels, and was only able to act as a shield bearer in the fight with the Fifth. Now, against the Sixth, I have also proven to be inadequate to the task. I must focus more of my time and energy on learning how to obtain an infinite synchronization ratio with my Evangelion if I am to have any hope of helping defeat the Angels. The Commander cannot be pleased with me and my performance. I must work harder to improve my piloting skills. I must not fail him.

She looked to the door as it opened and Dr. Akagi stepped through, pushing a cart before her.

Rei resisted the urge to sigh loudly. As much as she did not wish to deal with the doctor, there was nothing to be gained by letting her know this. Rei had so far been unable to find any evidence that suggested the woman was not operating under the guidance of the Commander. As such, she often relayed information from him. While she had not been entirely honest with the Commander a few times in the recent past and had attempted to circumvent his orders on the flimsiest of rationalizations (He had, after all, said the medical and security staff would be told that she could not see Ikari. He had not told her she wasn't actually allowed to do so), it would not be wise for her to potentially further anger the Commander by ignoring his some times proxy and mouthpiece.

Knowing this did not make it any easier for her to put up with listening to her Nemesis talk.

"Ah, Rei! You're awake! How do you feel?", her tone almost annoyingly chipper.

Rei stared at her, trying to decided on the best answer to the query. I feel like conducting proximity experiments on Ikari. I feel like conducting tranquilizer experiments on you. Even though both statements were valid responses to the doctor's query, Rei doubted the woman wanted or needed to hear them.

"Tired." came the soft reply, her voice barely above a whisper.

"Well, no doubt. You did give us a scare there for a little while, but you pulled through in the end with nothing more serious than a case of major fatigue. Now, I've got some good news and some bad news. What do you want to hear first?"

Rei looked at the doctor, trying to figure out what was normally requested first. She had heard the expression before, as it was used many times by various people in her age group and above, but she had never given it much attention, nor had she tabulated the various responses to it.

What metric is she using to determine the quality of the news? Both terms are nebulous and largely relative. An amputated limb is hardly seen as a 'good' thing, but when compared to death, there is a definite population preference towards amputation. Similarly, disobeying the Commander is 'bad' but not being able to see Ikari is more so. Good things are normally celebrated, while bad things normally require additional actions to compensate for them. Therefore, I should elect to receive the 'bad' news first, as to gain addition time to plan and react to it.

"Bad."

"Shinji is going to be in solitary confinement for quite some time."

That was indeed very bad news, as far as Rei was concerned. In fact, it rated up there with being used to suddenly decelerate particles on her sliding scale of 'bad' things.

She looked at the doctor expectantly, waiting for more information. With that as a baseline for 'bad', almost anything else that could possibly happen would most certainly be labeled 'good'. She suspected being told she would be living with the doctor would be considered comparatively good news, when using that metric.

"Good." she stated, wondering what condition Shinji was in, and what he had done to merit a stay in the detention block.

"Both Unit-00 and Unit-02 are almost completely repaired, so our ability to intercept and eliminate the Angels will be unimpeded. Also, on a side note, since you were asking about it before this mess got started, Shinji's cybernetic knee was installed successfully, and he is taking well to his new leg."

How long was I asleep? Was I placed into a coma as well? What purpose would that serve? I appear to have all of my limbs. Even if there were a point where my survival was in doubt, there would be no need for alarm, as all that is required is to decant a new body and transfer the image into it.

"Why is Pilot Ikari in solitary? When last I saw him, he was in a coma in the hospital wing. Also, how was the Angel defeated? Was it Pilot Sohryu, in Unit-01, as per the emergency plan? I do not remember what happened."

As if Pilot Sohryu could defeat the Angel. I know that it was Ikari. No one else could do such a thing, but it will be interesting to see if she will admit the truth. If she lies to me about this, what else is she lying to me about?

Dr. Akagi looked strangely at the girl, uncapping one of the many syringes lying on her cart. "You don't remember what happened? What's the last thing you recall?"

Rei did not wince as the hypodermic needle pierced her arm. She never winced at such things. It was a waste of time and calories, twisting and contorting one's facial muscles in response to a tiny needle in one's flesh.

"I was attempting to battle the Angel underwater when missiles threw me off course. My power ran out, and I sat in the Entry Plug until I lost consciousness." You do not need to know that I was thinking of Ikari. It is not relevant to you. She looked at the doctor as another needle entered her arm. "How long was I asleep?"

"Oh, not long, only a few days. So, that's all you remember? Nothing else?" Like calling for him when the medics dragged you from Unit-00? Nothing like that? Ritsuko thought to herself, as she plunged a third needle with professional quickness into the pale girl's arm.

"No."

"Ah, well, it appears that when he woke up, it was just as the Angel was spotted. When he found out you were the only one fighting it, as Unit-02 was still not mission capable, he freaked out and somehow managed to get himself into Unit-01, and activated it."

He was not fielded as an emergency measure by the Commander? He did this all on his own? Inwardly, she reeled with shock at the news. While she knew the boy seemingly disliked his father, piloting the Evangelion and fighting in general, she also had plentiful evidence that he felt something towards her, even if it was just an extreme protectiveness and an agreeable nature towards suggestions to partake of cuddling experiments when inebriated. He was very protective of her, but for him to go and launch himself, apparently only with just the information that she was fighting alone, well, that was a discovery of massive import. More research would have to be done on the events of the fight and their timeline. But this news also raised new questions that could be answered immediately by present test subjects.

"Why is Pilot Ikari in solitary confinement if he was successful in the destruction of the Angel?"

"Because he launched without proper authorization, and because he tased his security escort."

He did what?

Taking the used needles and placing them within the sharps container, Dr. Akagi then handed Rei a new vial of pills. "Well, take these once a day with water before bed. We'll keep you here tonight for observation, but I'm sure you'll be back home on the surface tomorrow. Do you have any questions?"

"I need to see the video recordings of the fight, in order to further my own combat abilities against the Angels."

Dr. Akagi smiled at her, hands on her hips, studying the girl. Oh, do you now? Or do you just want to see what all your little 'boyfriend' did on his rampage? Well, I'm afraid you're out of luck on that matter. "Unfortunately, we had to initiate the Gomorrah Protocol, in order to keep SEELE in the dark about what was going on. By the time our systems came back online, the battle had moved to outside the view of the surviving sensors."

Rei said nothing more, and Dr. Akagi left the girl to her thoughts.

If they initiated the Gomorrah Protocol to hide Ikari's actions from SEELE, then it means that he was rampaging, and thus not controllable. This does suggest that he deployed Unit-01 on his own initiative, which also is supported by the roars of Unit-01, which had only previously been present during the so called 'Berserker' mode. How will they explain to SEELE the effects of the EMP weapons? It could possibly be blamed on the Angel. The battles with this Angel already had been unorthodox and deviated significantly from the previous encounters. With the already considerable deviation from the past Angels, what is one more ability? After all, if they cannot alter their mission parameters, they would be useless without support from other entities.

That thought struck up both fear and interest in her. Could it be that the Angels learn from each failed attempt? This is the second Angel to hide its core within its body, and both times, the Angel was harder to destroy. This Angel is also the first one to have retreated, instead of attacking until it could do so no longer. Will future Angels employ such tactics, and improve upon them?

Hypothesis: Each Angel develops itself based on the abilities, successes, and failures of each one that comes before. This is somewhat supported in that the Angels have the ability to regenerate at a tremendous rate and can learn from their successes and failures in the immediate battle, either with the UN of JSSDF forces or the Evangelions. Other than waiting to see how the next Angels act, I do not think there is any way for me to test this. I should talk to the MAGI, and see if this has occurred to them.

I will need to speak to Ikari, and find out what he remembers of the fight. But... He does not like to discuss such things. I do not think he will be amicable to the idea of speaking on the issue. But I want to know what happened...

Rei felt new irritation and annoyance blossom within her. The Gomorrah Protocol might have hidden the fight from SEELE, but it was also working against her. She had to see what had transpired, especially now, if she was to check the tactical abilities of future Angels against the past fights, in addition to her own ongoing research into Ikari's hypothetical ability to become his Evangelion. But at direct odds with this was a new need and wish not to see him upset, something she told herself was only because she did not want to skew future experiments of physical proximity with him, as he was the only person in her age group that was not already biased against her.

He must not have been badly injured if at all in the fight if he was injured at all. Especially if they already have the new knee and leg attached to him, and he is at the same time currently incarcerated. The last time they did that, they waited until he was cleared from the medical wing. I wonder what the specifications of his new knee and leg are. I will need more data on the fight in order to determine if the loss of his leg interfered at all with his piloting.

I wonder if I request leniency for him from the Commander if he will allow him to go free? She did say he was going to remain in solitary for 'quite some time,' which, during an imprecise measurement of time, does seem to be used in cases where an extended period of time is expected or experienced. What would be appropriate arguments for his early release? He did defeat the Angel, which is why NERV exists. He allowed for the successful rescue of NERV personnel that he did not know to be immediately replaceable. He allowed for the successful recovery of vital NERV equipment, namely Unit-00. She even said that it is almost completely repaired. Surely this all outweighs merely tasing some Section 2 agents?

She closed her eyes but sleep refused to come. Unsure what was bothering her, Rei looked around the room again, not knowing what she was looking for. At the base of her skull, buried in the deep recesses of her mind, something screamed out that there was something missing. Closing her eyes and collapsing back onto the pillow, she decided to ignore it and began instead to think about a shirtless Ikari embracing her.

Eins, Zwei, Drei, Vier!

"This is unacceptable, Ikari." the monolith labeled only as SEELE 05 intoned, the distorted voice still able to sound irate despite the heavy modulation of the anonymity filters.

"This is a disaster. The Angels are to be defeated, not allowed to escape, and then return to cause more destruction. The costs to the already damaged defense systems of Tokyo-3 are almost incalculable."

"Worse still is the damage done to the Evangelions and the Pilots. They are two halves of the same coin. One will not work without the other, Ikari. With two Evangelions damaged and undeployable and one Pilot damaged and unable to pilot, if another Angel were to strike, it would be the end of all things."

"The Third Child is perfectly capable of piloting. The surgery went well, with no complications, and the Pilot is responding well to physical therapy. Evangelion Unit-01 stands fully ready to defeat any Angel that may come."

"Why, then, has this information been withheld from us?" The surprise was evident in SEELE 07's voice. "If he has been released from medical, the report should have been filed."

"He has not been released from medical; he is still in the initial stages of physical therapy and remains at NERV." Gendo reached out to push his glasses back up onto his face. Having pushed off the meeting with SEELE until after the Angel had shown itself had been a risky choice, as the old men were not happy at all with Gendo. However, they could not publicly fault him for the excuse, as he had thrown all of NERV into a full-throttle search for the Angel, in addition to making repairs to the Evangelions and the external defenses of Tokyo-3.

So far, his decision to invoke the Gomorrah Protocol appeared to have had the desired effect; at least, they publicly accepted the lies that ran through the reports delivered to them about the new abilities of the Sixth Angel, Gaghiel. Gendo knew, however, that there was a very real danger and possibility of them knowing about the actual events of the battle. He was still waiting on news from his agents close to the old men to finish their reports. Until then, he would have to tread more carefully than was normal.

SEELE 01, Kiel Lorenz, the mastermind and progenitor of the plot, spoke up and put an end to the general chatter the conference had devolved into. "At any rate, the next Angel is not due for some time. Ikari, you need to ensure the Angels are destroyed more efficiently in the future. If you do not, we may consider replacing you as NERV's Commander."

He said nothing in return, passively listening as SEELE 06 made a snide comment about possibly promoting Fuyutsuki. The monoliths disappeared from view, leaving him in darkness. He stood and left the room, passing his second-in-command without a word.

"I expect the meeting went as we imagined," Kozo commented, noting the clenched jaw. "Do you think they suspect anything? Or have evidence of what actually happened?"

"No. Everything points to them being in the dark as to the true events of the battle."

"Then all is as well as it could be, I suppose. I do have some good news, however. Rei's woken up, and other than not remembering what happened during the fight after the missile launch, she seems to be fine." He paused, taking another glance at his friend. "She did ask after Shinji. Dr. Akagi told her where he was."

"Has she made any efforts to see him?"

"No, she went back to sleep shortly after receiving the medication. But I'm sure it's only a matter of time before the attempt is made."

"See to it that security knows she is not to see him." They walked in silence, and neither spoke again until they entered his office. Taking his seat and pulling a report detailing the cleanup progress, Gendo glanced at the older man. "Did she ask about tapes from the battle? If she has no memories of it, I'm sure she must be interested in finding out what exactly happened."

"She asked after them, but Dr. Akagi informed her that due to the Gomorrah Protocol, there are no records of the fight after the detonation of the missiles."

"Good. Have the MAGI come to a conclusion yet?"

"Dr. Akagi reports they are still undecided and are withholding judgment at this time."

"I'm not sure if to be worried or comforted by the fact that they find what happened as incomprehensible as we do. Has the security restriction to the files concerning the battle been activated yet?"

"Yes, it's already in place."

Gendo pulled a video still from underneath the paperclip that held the report together, studying it intently, although he held no hopes of divining the answers he sought from it. It showed a storm-ridden sky over the Bay of Tokai, which was strangely empty of water. Two blurred figures, one of purple and the other of white, locked in battle along the slope of the now-dry sea floor.

Vier, Drei, Zwei, Eins!

Frost formed on the metal armor of the Evangelion Unit-01, The Berserker. Small pieces of ice began to form in the water, surging around its waist, and rain became sleet as the Evangelion became a massive endothermic engine of death and destruction, ripping the very heat from the environment around it to stoke the fires of its fury.

With a scream that was the sound of a wailing wind as it passed through the Valley of Shadow of Death, the Berserker threw its arms up high into the air and slammed them down again onto the water, its fists trailing icy fog through the rapidly cooling air.

Yellow hexagons flashed into and out of existence in the second of impact, and the water inside the bay became the same icy fog and then vanished, dissipating quickly into the warm air. At the mouth of the bay, a wall of water stood unmoving, a line delineating the extent of the Berserker's AT-Field. Had there been any sea life that had not fled before the approach of the Angel, and then the coming of Unit-01, the dry seabed would have been scattered with imminently surprised creatures. As it was, Unit-00 crashed down onto the sloping ground to roll to the bottom, and the shocked Angel did likewise.

However, Gaghiel was no mere fish, its resemblance to one non-withstanding. It was an Angel, and as such the mere alteration of the environment in which it had been was of no real concern to it. It wasn't entirely present in this dimension; it belonged to a classification of beings so far removed from man that, under normal circumstances, there would have been no hope for the puny offspring of Lilith to battle it. Massive flippers shifted as bones stretched and broke into new configurations. As it got to its feet, it looked up with a toothy grin and glowing eyes just in time to see the Berserker crash into it; harpoons held up to the raging sky.

Fire burned in the eyes of Unit-01, bellowing in triumph as it wrapped its legs around the Angel in a bizarre approximation of a choke-hold, raining blows down into its flesh with the harpoons, ripping chunks of pale flesh out each time it raised its hands back up to strike again.

Screaming in rage at this indignity and affront to its being, Gaghiel staggered back and forth, attempting to beat its attacker off of it. The now all too familiar cross-shaped pillars of light, that common weapon of the Angels, erupted once more as its cries became more and more plaintive. Fires began to spread on the beach where the pillars hit buildings and equipment, and large sections of rocky sand became blackened glass.

Tiring of the ineffectiveness of its attacks, Unit-01 allowed itself to be thrown from the Angel, rolling into a crouch a few hundred feet from the leviathan. Enraged, the Angel unleashed its energy weapon again, scoring three direct hits on the Evangelion as it began to run back towards it, seemingly uncaring about how the paint bubbled and burned, the smoke and flames somehow not affecting the frost and ice now several inches thick in places along its armor.

A fourth cross hit Unit-01, this time in the face, sending it crashing backward, head over heels into the ground, gouging out a trench in the soft earth. Unseen by both combatants, the wall of water shook as if it were a door someone had slammed their shoulder up against. Ripples were visible to the naked eye as they traveled across the surface of the wall.

The keening wail returned now in full force, as Gaghiel was sure victory over this new foe was now near. It began to make its way over to where the titan lay, its gigantic plodding pace eating up the distance. It opened its mouth wide, teeth flexing outwards, as it made ready to consume the stricken giant.

Fire burning in one eye and blood streaming from the ruined socket of the other, the Berserker howled again as it rose up from the earth, hands outstretched greedily for the red orb sitting in the back of the enormous mouth. Realizing too late the danger, Gaghiel clamped it's mouth down suddenly on the arms, teeth piercing through the armor and the flesh that lay beneath all along the upper arms of the Evangelion. Blood spurted up high into the air as the Angel's jaws shifted and clenched, Unit-01 held trapped in its mouth as surely as a mouse in a cat's jaws.

Strangely, the Berserker made no noise as it twitched, the entirety of its body convulsing minutely. The wall of water shook again, yellow hexagons flashing in and out of view, before vanishing altogether. The sea reclaimed the bay, washing over the titans, still locked together in a grim embrace with the roar of an avalanche. Waves splashed up and over the beach with furious energy, battering what remained of the established fighting position. The men and women who had ventured outside in an attempt to find out what was happening looked first at each other, and then with growing dread at the rolling waves.

It came suddenly, the cross of light shooting up high into the sky, this pillar larger than any of the others unleashed by the Angel in its fight with the Evangelions. Water exploded up and became steam mixed with smoke, quickly becoming an icy fog that hung over the sea. Fire and burning chunks of fish flesh began to rain down out of the sky.

Then, like a primordial god of old, Unit-01 rose up out of the sea, Unit-00 held in its arms in the manner of a groom with his bride. Water poured down off of the two cyclopes in great rivulets, doing as much to drive the men and women back into their shelters as the earth-shaking steps of Unit-01, as the beach turned into mud.

Frantic calls were being made over secure wire lines from the beachhead back to the command deck of NERV-Central, sending news of the apparent outcome of the battle. Emergency crews were dispatched, and Tokyo-3 began to shift into a stage four alert as damage control crews surfaced from below to determine the extent of the damage wreaked upon the fortress city.

With a strange gentleness at complete odds with the terrible violence it had just meted out, Unit-01 placed its blue companion on the ground before arching its back up to the sky; arms spread apart to howl its victory into the sky as if daring a response from the heavens above.

The fiery glow faded from its good eye, and the titan crashed to earth, its internal batteries expended.

From the moment of activation to the time it came to rest at the feet of Unit-00, it had been operating on the internal batteries. It had been ten minutes from start-up to shut down.

Eins, Zwei, Drei, Vier!

Shinji Ikari had a migraine headache. It was the first time in his life he had one and had he more experience with them; he would have been much more appreciative of the fact that he was stuck in solitary confinement, sitting there alone in the darkness, silence wrapped around him like a blanket. Even the sound of his own breathing was too loud, as did the sound of his pulse, felt with each throb of his brain at the front of his skull. He was also glad of the cool metal floor, as he rested his forehead against it.

As he drifted in and out of blessed sleep and the relief it brought him, he had no idea as to how long he had been down here in NERV's dungeon, and for the most part, he didn't care, the feeling of spikes being driven into his eyes erasing all other thoughts from his mind. He remembered being told Rei was safe, apparently fine with no injuries from the battle more serious than exhaustion and some bruising. He only vaguely recalled waking up with a metal attachment on his leg, and then later a skeletal, metallic leg and foot.

If anyone had shouted at him over launching Unit-01, he didn't remember it. It probably wouldn't have done any good, anyway. The door opened suddenly, and he winced and turned away from the lights of the corridor. Someone stepped lightly into the room, kneeling down next to his side, rolling up his sleeve. Cool liquid was swabbed onto his arm, just before a sharp pain shot through him as the needle pierced his skin. He winced again as his hair was tousled by a gloved hand before the unknown person stood and left the room, which was once again plunged into darkness as the door closed.

Eins, Zwei, Drei, Vier!

Rei found Hikari, Toji, and Kensuke crowded around her the moment she stepped into the classroom. Halting in the doorway, unsure as what to do, she had difficulty hiding her surprise as Hikari grabbed her by the arm and dragged her over to Shinji's desk, gently but firmly pushing her into it.

"Rei, are you alright? How's Shinji? What just happened out there?" the class representative asked, her voice low but frantic, waving an arm at the window and the cityscape beyond, where construction crews worked tirelessly and joyfully to rebuild the fortress city.

"I have suffered no permanent damage. Ikari is... Ikari's status is currently classified. As for the battle... it was a very difficult affair."

"What was that horrible scream? We all heard it, even deep in the shelters. I've never been more frightened in my life. Was it the Angel?"

Rei only stared at the girl, who was sitting close to her, her face much nearer than was the norm, mere inches away. She heard the scream of Unit-01? Where was the Evangelion when it screamed? The shelters are supposed to be sound-proof in addition to protecting against the debris of the battles. If it managed to be overheard inside the shelters, it would have been still some ways from the shore, but I heard it with no problems within Unit-00, underwater, during a storm, while fighting the Angel. I must talk to the MAGI tonight.

"That information is classified."

Toji put his hand down gently on the desk, drawing Rei's attention to him. Looking straight into her unsettling red eyes, he took a deep breath. "Rei, we're asking because we're worried about Shinji, and about you. Ken still won't say anything about what happened on the ship, but I know that whatever happened, it couldn't have been good. Then, this last battle happens, and you're only now just getting back to class, and the Shin-man's still missing. We know, at least a little," he said, his eyes darting to the other students warily before returning to lock gazes with the strange girl, "what it's like in the cockpit. You feel what happens, and... strange things happen to you when you pilot. I saw the red one when it came in. It was missing a leg! He was piloting it when it happened, wasn't he?"

Rei shifted slightly in her seat, broadcasting to anyone well-practiced in Rei-watching that she was unhappy. She blinked twice, and with the faintest twitch of her eye, she expelled the breath she hadn't been aware she had been holding.

"He was piloting it, along with the regular pilot. She escaped without harm; he was the only one who suffered. During the last battle... he came to my rescue when the Angel managed to overpower my Evangelion. I am told he is fine and suffered no further injury, but he is being held in the detention block at NERV."

Hikari gasped, clearly shocked by the news. The boys had not told her much, nothing really, about the Evangelions, being loathe to tempt fate and invite trouble into their lives. Kensuke breathed a sigh of relief, glad that the secret he had been forced to keep for the past few days was out, and by someone else than him. Toji swallowed hard, not wanting to continue, but now he had more questions to ask. He could, as he had done in the past, simply ignored the issue, but he held himself to a stricter code than that. Shinji needed a friend, and he would be a friend. And friends didn't let friends rot in jail for saving the world; at least in his book, they didn't.

"The detention block? What? Why is he there?"

"He tased his security escort and launched Unit-01 by himself, without prior authorization."

Triplet looks of incomprehension locked together and then turned back to Rei. Hikari found her voice first and asked the question burning in their minds.

"He did what?"

"When he was informed I was fighting the Angel by myself, due to the damage done to Unit-02, and him being in the medical wing, he assaulted and incapacitated his security escort and managed to gain entry to his Evangelion, and launched himself. He defeated the Angel shortly after engaging it."

"And for that, they locked him up? That's bullshit!"

"No, it is the truth."

"When are they going to release him? Isn't there anything anyone can do?" Hikari asked as the boys shook their heads. What could anyone hope to accomplish, going up against the will of the ones who ran the entire city, and fielded monstrous giants with children for pilots as a matter of policy? Who was going to tell them they couldn't do as they pleased? A group of high schoolers?

Rei confirmed their dour outlook on the situation with a shake of her head. "The order for his incarceration was given by Commander Ikari himself."

"His own father?"

"Yes."

"What about Misato? Surely she can do something! She's the Operations Director! She can't just stand by and let something like this happen!"

Eins, Zwei, Drei, Vier!

Misato stared at the battered form of Evangelion Unit-01, held in heavy shackles in addition to the normal locking restraints, the crucifix-shaped signal terminator plug firmly lodged in the socket that would normally house a normal terminator plug, or the Entry Plug of its chosen pilot, Shinji Ikari. She turned to her long time friend, Ritsuko Akagi, never taking her eyes from the behemoth.

"Are you sure it was Shinji? I mean, it wasn't someone else?" she asked, her voice thick in disbelief. "I have a hard time seeing him getting the drop on two secrecy service agents, getting all the way up here, and then manually activating and launching his Evangelion. I mean, we're talking about Shinji for crying out loud!"

"It was him. There's no doubt about it. We've got the MAGI's security tapes showing him the entire way up." She scowled, but her tone remained strangely light, considering the situation they were in. "Of course, the only way he was able to get Unit-01 to launch was because we had it prepped on emergency standby status for Asuka, in case we needed to try to field her."

"What about it's weird behavior?"

"What do you mean? The screaming? That's nothing new. It normally does that when it goes into Berserker Mode, you know."

Misato frowned at her friend, fully turning her face to her, as Ritsuko ignored her look, industriously studying the report attached to her clipboard. "Yeah, that's pretty freaky, but I'm talking about how come it was able to run for ten minutes with no power?"

"That's impossible, Misato."

"I know, that's what I'm saying."

Ritsuko, pulling herself away from the report, turned to give the Operations Director an unamused look. "It didn't run for ten minutes without external power if that's what you're trying to get at. He obviously hooked up to Rei's cable after it was ejected."

"Witnesses say it didn't have one when it came out of the water."

"Obviously it had to eject it to go get Unit-00, and more importantly, I think to him, Rei."

"You know, if she doesn't jump his bones after this, I think he's going to stop rescuing her."

Everyone within earshot of Misato's offhand and slightly off-color comment slapped a palm to their face. Ritsuko, groaning in exasperation, stared at her friend through the spread fingers of the hand plastered to her head. "Are you serious? Did you really just say that?"

"What?" Misato asked, shrugging. "I mean, how much more would a guy have to do for you in order to get you into his bed?" She groaned now, a wince crossing her face. "You know, we still need to give them the talk."

"The Commander has him locked up in solitary, and you're concerned with giving them the talk."

Misato shrugged again, once more seemingly free from worry or care. "I'm not happy about it, but... He did assault his security officers, and anyway, he can't keep him down there forever. Not when he can competently do visceral things to the Angels."

A new pain blossomed in Ritsuko's brain as Misato tried to bludgeon her way through the conversation. "I think you mean 'completely ruin their shit'? If you're going to quote somebody, can you please do it right?"

"What? What'd I say?"

Eins, Zwei, Drei, Vier!

Maya tried not to glare at the girl, busily typing away at the MAGI terminal. She had been less than enthused to meet the newest addition to the pilot corps. The energetic German girl apparently had done nothing but win praise and adulation from Dr. Akagi while she had been with Captain Katsuragi, which rankled the lieutenant, who had worked hard to be assigned to the almost legendary doctor's immediate staff. But as she observed Asuka studying the information flashing across the screen in response to the inputted computer queries, she did have to grudgingly admit the girl was good and had potential.

I still don't see why she's taken to calling Sempai Sempai so fast. When are we sending her to the school for socialization? The less she's down here the better. But... she does seem to have earned that degree in her records. And she's truly interested in what's going on and what happened. Maybe it's just that she's so different from Shinji and Rei. Yeah. That's got to be it. I'm just used to the pilots being so introverted; it's a shock seeing someone so full of energy and so outgoing instead.

Maya watched the girl for a few more moments before turning back to her own work, but not before wondering where she had seen that lab coat before. It wasn't Dr. Akagi's, as she was almost never separated from it, but she was sure she had seen someone else wearing one around the place before. While there were researchers aplenty here in NERV-Central, most eschewed wearing lab coats in favor of utility uniforms.

Asuka watched the pretty brunette tech out of the corner of her eye as she worked. She had expected the likes of Lieutenants Hyuga and Shigeru to be in plentiful amounts, typical technicians the both of them. Completely uninteresting, much like the other two pilots. Excepting, of course, the bizarre behavior of Shinji Ikari in this last battle. But as for Maya Ibuki, well, Asuka was struck by the woman's attractiveness (but not as attractive as her, of course) and the skill that hadn't been as over-exaggerated as she had thought when Dr. Akagi introduced them.

She's very good. Almost as good as Sempai is, I think. I can learn much from her too. She looks so young, too! She can't be that much older than I am. Oh, I wish I didn't have to start going to that stupid school soon. I'll learn so much more here, than there! What can I learn sitting in a class full of boring, stupid children?

Her train of thought was interrupted as the MAGI flashed some new data at her, which completely contradicted everything she had thus far found out in three different ways.

That's so strange. Even the MAGI doesn't know what to make of the data feed from Unit-01 during its rampage. All this data is junk! Why doesn't anything about this whole thing make sense? It's like Unit-01 is nothing at all like my Unit-02 or even Unit-00! Shiesse! Now what?

As she cursed under her breath and in her head, a new error message flashed on the screen; the MAGI stated she lacked the necessary security clearance to view the design specs on Unit-01. As she had the clearance on the specs for Unit-02, this new mystery caused her to throw her hands up in the air in frustration. She had also heard mutterings that Unit-01 had run amok above ground for ten minutes without external power, and while she knew it was impossible, with all the other oddities that seemed to revolve around the Test-Type, she wanted to see if it was at least theoretically possible.

After all, she thought with a grin, if there was the smallest chance of me being able to do that in my Unit-02, then I ought to know about it, nicht? And if that dummkopf down in lockup can do something like this, well then so should I. But not that screaming thing. That was a little... too much.

She shivered slightly, the memory of the screams raising goosebumps on her skin. A thrill ran down her spine, and she could almost feel the awful vibrations of that roar in her bones, freezing her marrow. The fact that the thing had managed to break the jaw locks open was astounding. The heavy-duty metal restraints were screwed into the jaws of the Evangelions, clamping them shut. Unit-00 and Unit-02 went farther still, with full metal mouth guards encasing the entirety of the mouth and jaw area, foregoing the stylized bared teeth pattern that adorned Unit-01. It was, as Asuka noticed, yet another difference between it and its predecessor and successor. But she refused to let this setback keep her down.

And so she keyed a new query into the terminal and began again. No matter how long it took her, she would get to the bottom of this mystery. There was nothing that the Great Asuka Langley Sohryu could not do or figure out once she put her wonderful mind to it.