Gendo Ikari and Kozo Fuyutsuki were the only living figures in the darkened NERV conference room. They were accompanied by holographic displays of SEELE's leader, who appeared in the rather anonymous form of black pillars marked with red numbers. The entire set-up resembled something between a teleconference and a Satanic ritual.
A deep voice rumbled from SEELE's central pillar.
"The EVA-04 disaster has caused America to back out of the Evangelion program. This leaves NERV's Japan base as the only properly equipped launch site for EVA-03."
Gendo sat with his elbows on his table and his hands crossed under his nose. He didn't like where the conversation was heading, but he had already thought of an escape plan. He replied with what he hoped would be interpreted as professional advice.
"The resources we would spend shipping the unit and running the activation test could be better used finishing the upgrades to EVA-00. I suggest we go the latter route rather than clean up another country's mess."
The SEELE pillar shot down his efforts quickly and coldly.
"No. EVA-03 is a state of the art machine and will be much more useful to you than that outdated model. Since the other candidates are currently assigned to active units, EVA-00's pilot will left with this responsibility."
Gendo gnashed his teeth behind the curtain formed by his folded fingers, but replied in the most obedient tone he could manage.
"Very well."
Light abruptly returned to the chamber after each of the holograms disappeared, revealing the place to be somewhat of a fall-out shelter with Gendo, Kozo, and a small table as the only occupants.
Fuyutsuki, who had been standing behind and slightly to the side of his superior with his arms folded behind his back, now gave a look of grave concern. He spoke in private with Gendo, knowing he was no longer under the scrutinizing eye of SEELE.
"Are you really going to make Rei pilot it?"
Gendo replied as he continued to stare forward, hands still crossed over his mouth.
"We have no choice. If we push back too hard, they'll start getting suspicious."
"What if this ends like the EVA-04 incident? If we lose her..."
Gendo interrupted his second-in-command in the same collected manner.
"I knew from the start this wouldn't be completely straightforward. If there's one thing Yui taught me, it's that sacrifices must be made for progress. We're going to have to put our security aside and rely on a gamble sooner or later."
His eyes gazed down toward the empty table while he took a brief second to adjust his strategy.
"SEELE is becoming too demanding with their plans. We must hasten EVA-01's evolution."
Fuyutsuki questioned this statement with an air of concern.
"But how can we accomplish that? It's already been months, and Rei and Shinji are barely beginning to bond."
"There's one possible catalyst we can use if the proper conditions arise. It's dangerous, but we may have already lost the luxury of having options."
Gendo paused again to run a few possible scenarios through the back of his head. When he resumed, Fuyutsuki noted he had never heard his Commander sound so doubtful before.
"The only thing that can help us now is a blessing in disguise."
Shinji Ikari was in trouble. The respective red and green Evangelions of recent newcomers Asuka and Mari were disheveled across the battlefield, with their pilots most likely teetering on the brink of consciousness. He was left alone to experience the displeasures of slowly being strangled to death by the latest Angel through his mental link to EVA-01. This particular Angel had possessed EVA-03's semi-organic body during the unit's disastrous activation test.
As Shinji exhaled another flood of LCL bubbles between his gagging breaths, he heard Gendo's voice reprimand him through the static of his cockpit radio. Father and son soon entered a heated debate.
"Shinji, why do you refuse to fight back?"
"Because Ayanami is in that thing!"
"But it's an Angel. It's your mission to destroy it."
"I'd rather let myself die than kill someone else!"
In NERV's headquarters, Gendo was carefully watching the battle between EVA-01 and the Angel through the base's wall-sized monitor. He was seconds away from facing the moment of truth. When he heard his son refuse his orders for the final time, he shifted his cold words to the row of battle technicians seated below him.
"Then it's settled. Activate the Dummy Plug System."
Maya swiveled around in her chair before frantically responding.
"But sir, we've only completed 60% of the trial phase!"
Gendo gazed downward from his command pedestal before he impatiently reiterated his command.
"An untested solution is still worth more to us than a child having a temper tantrum. Activate the Dummy System, NOW."
He also had another reason for this level of commitment. The monster's female hostage was probably moments away from being fully assimilated by the cellular structure eating through EVA-03's Entry Plug. If an Angel successfully joined with a daughter of Lilith... No. Now wasn't the time to pointlessly worry oneself over worst case scenarios. He had to stay focused.
Maya shyly nodded before turning back to her console.
"Ye-... yes, sir."
Shinji gasped when EVA-01's cockpit switched to emergency lighting and the sensation of bestial fingers crushing his throat faded away. He could still see EVA-03 on the screen in from of him. Its limbs were grotesquely warped by the Angel's influence, with its elongated arms reaching forward to grasp EVA-01's neck.
Before long, a new sense of shock overwhelmed Shinji. He could feel EVA-01 shudder back to life on its own will. He went as far as repeatedly struggling with his cockpit controls before he thought aloud, unaware no one would answer him.
"What's going on?"
EVA-01 reached forward and wrapped its hands around EVA-03's armored neck, now under orders from its unseen commander. The two Evangelions mutually tried to choke each other into submission before EVA-01 took the advantage and climbed back to its feet in a display of superior strength. Simple showmanship wasn't enough to satisfy its cannibalistic appetite, however, and it continued to squeeze EVA-03's throat until its head buckled sideways and the synthetic vertebrae in its neck snapped into pieces. The Angel's arms immediately fell limp before EVA-01 roughly tossed its body to the ground.
Shinji's eyes had become filled with horror as he stared at the Angel-Evangelion now sprawled across the ground. He could tell his own EVA had somehow been taken over by an animalistic nature, and now EVA-03 and the pilot trapped within were both helpless to the impulses of an unbridled beast. He screamed into his radio as EVA-01 ominously leaned over its prey.
"Why are you doing this, father? Can't you see the EVA is just going to tear her apart?"
EVA-01 then pulled its arms back with the obvious intent of crushing EVA-03's motionless head like a pimple. Shinji objected further as he made another futile attempt with his controls.
"Stop it! Just stop it!"
He clenched his eyes shut and dropped his head in grief when he was answered by more radio silence. He nearly broke into sobs as he weakly mumbled.
"If you make me kill Rei, I won't be... human... any more..."
After speaking these words, Shinji went through a transformation of his own. His expression changed to one of rage. When his eyes opened, they glowed with an unnatural radiance that was all the more evident in the dimly lit cockpit. He firmly took EVA-01's controls into his hands with a new, much more forceful determination as he breathed in what can only be described as guttural snarls. At the moment the concern he held for Rei's life was the most intense, he had become a different person.
On NERV's display screen, EVA-01 suddenly froze in mid-attack. The base personnel watched as the unit slowly lowered its arms back to its sides, and Maya soon reported what she was observing on her monitor.
"Commander Ikari, something is interfering with the Dummy Plug's signal! It's lost control of EVA-01!"
A new flood of data streamed across the computer screen before she shouted with increased urgency.
"It... it's being overridden by Shinji's neural waves! He's re-synchronized himself to the manual controls!"
Gendo narrowed his eyes in contempt before barking orders.
"Try to restart the system! I don't want the Angel having a chance to escape just because our pilot had a morality attack!"
He knew it was a lost cause, though. He simply needed to continue to play his character as a formality, as nothing could take away his son's newfound independence. Behind crossed hands, he smiled to himself and muttered at a volume only he could hear.
"It was about time you cut the apron strings, Shinji."
Shinji had to rescue Rei. That was only the only thing that concerned him at the moment. His father could have all the fun in the world butchering the new Evangelion unit as long as it didn't conflict with his own interests. For what it mattered, it wouldn't have made any difference to him if the Angels took over and destroyed everything. He had to make sure Rei would be out of harm's way first.
EVA-01 lifted EVA-03 into a seated position so its back faced the open air. Shinji directed his EVA to look over the sister unit's black shoulder armor, allowing him to see the cockpit hatch had become overgrown with a sort of neon blue fungus. He used EVA-01's arms to reach toward the strange growth, intent on yanking the steel cylinder from its holding plug and freeing the pilot from its captor. The moment EVA-01's hand took hold of the Angel-infected Entry Plug, however, something mysterious happened.
Within EVA-01's cockpit, reality as Shinji knew it melted away. The camera screens instantly went dead and the interior walls faded from sight, leaving him floating in an ochre-colored nebula that seemed to expand infinitely in all directions. In the distance, he could see an amorphous formation of the same glowing blue matter that had imprisoned EVA-03's Entry Plug. As he began swimming toward this object, he heard sound of children's laughter echoing through the space around him. He didn't let the eerie noise bother him, however, as his mind was focused solely on one purpose: Rescuing Rei Ayanami. Nothing about this strange shift in environment was enough to make him forget why he was here.
When he was close enough to the glowing mass, Shinji realized he had found his target. Rei was asleep, crucified to the invasive entity as it took the shape of an improvised Tree of Woe. It had seemingly grown around her, enveloping most of her body in its gelatinous material. Only scant remnants of a white Test Plugsuit clung to her skin, as most of it had been digested by the alien structure. It was hard to tell whether she was becoming part of the Angel or the Angel was becoming part of her.
Rei somehow sensed Shinji's approach and began to stir. When she looked toward her visitor, her voice held a hint of sadness and her usually stoic expression gave way to slight shame.
"Why have you come here, Shinji?"
Shinji propelled himself further through space so he was nearly close enough to reach for her.
"To save you!"
Rei looked away when she replied. Had her movements not been severely restricted, she would have probably turned her back to him.
"What's the use? I'm your enemy now."
Shinji shook his head as he tried to turn his anger into inspiration.
"Don't say that! None of this is your fault!
Just when Shinji would have reached Rei, the Angel took defensive measures to protect its precious treasure. A series of vines burst from the gel-like substance and tried to either impale Shinji or push him away. In either case, Shinji pushed through the attack with even more strength than before. He had made up his mind he wouldn't let anything separate them.
When Rei weakly spoke again, her words sounded empty and robotic. She would have shown concern toward Shinji's predicament if she had the emotional capacity to do so.
"You should kill me before I bring you any harm. They can just replace me."
Rei's willingness to sacrifice herself for others only gave Shinji more resolve to keep her safe. He batted his way through another wave of vines as he shouted.
"I don't care!"
More of the Angel's defensive wall shot forward. Shinji was becoming more and more entangled in the translucent substance with each inch he moved forward, but he remained relentless.
"I don't care about any of that!"
Finally, he reached Rei. There was nothing left to keep him back.
"You're the only thing I care about!"
Shinji launched himself forward to wrap his arms around her shoulders, embedding part of himself into the Angel in the process. Rei's somber attitude ended as she widened her eyes in surprise.
EVA-01 slumped forward like an abandoned shell the moment contact was made. After this happened, EVA-03 (or whatever entity was now controlling it) growled with rejuvenated life. It violently reached forward to impale EVA-01 through its breastplate and embed its hand in the unit's lifeless husk. With EVA-03 holding EVA-01's core and EVA-01 holding EVA-03's contaminated Entry Plug, the two adversaries were engulfed in a blinding flash. In their place stood a single entity, a humanoid giant made of streams of light. It was as majestic as it was terrifying.
The sky turned blood red. Living matter disintegrated. Bodies of water evaporated. Buildings floated into the air as rubble. The new creature's AT Field nullified the effects of gravity at its point of origin, and its domain was slowly expanding.
This was the Third Impact. The world was going to end.
And then Kaworu showed up in EVA-06, threw the Lance of Longinus, and did his "This time I'll make sure you're happy Shinji" thing The End.