Third Genesis: Endgame

Misato moaned in pain as she came awake, leaning against the control panel as alarms wailed through the underground complex that was NERV. Something had tripped every alarm, and the staff had fled the structure and raced up into Megatokyo, even as Misato went to the command center to find out what was wrong.

"I see you're coming to," the calm voice said, "I was worried I had injured you when I knocked you out."

Misato turned herself over, blinking as she tried to clear cobwebs from her brain. "Yui?" she asked, looking in confusion at the woman trapped in a boy's body.

Yui Ikari had a gun in her hand that she held with a eerie calm, her gaze oddly kind as she said, "I'm sorry I had to strike you, but I needed your fingerprints to clear some security lock-outs."

Misato made herself stand, shaking off her dizziness as she grimly demanded, "What are you doing, Yui?"

"I'm removing my life's work from the world," Yui shrugged. She raised her voice, "Magi, is everything in place?"

The artificial voice of Naoko Akagi answered calmly, "The bombs are prepared, as are the bioweapon modules. Detonation in twenty minutes."

"Come on," Yui gestured for Misato to go to the elevators, "it's time for you to go."

Misato pushed herself away from the terminals, a splitting headache making thoughts hard to assemble. "Damn it, are you destroying NERV?" she demanded as they walked.

"Yes," Yui answered as she walked her to the lift on gun point, "my work has only caused death and destruction, Misato. It's time to end it."

Misato looked back at her compassionately, "You're not at fault for what happened to Shinji or that mad girl, Nao Rokubungi."

"If not me, than who?" Yui answered as she waved Misato into the elevator. Calmly she added, "And don't try to jump me, Misato. I really don't want to shoot you."

Misato met her eyes and realized she was dead serious. "Please don't do this," she said gently as she went inside the elevator.

"Goodbye," Yui said simply, closing the doors with a press of a button.

Yui Ikari walked back to the command center of NERV, the building surprisingly quiet without all the staff that kept things running. As she settled into the seat, the magi spoke up again. "I can still get you out before detonation, Yui," Naoko said quietly, "you don't have to die here."

"Yes I do," Yui answered quietly, "at least if I want it all to end. I know too much." She smiled sadly, "Even without samples of a Angelic life form I could probably recreate a Evangelion, or something very like it. No, if I want this to end I have to go with it."

"I don't want you to die, Yui," Naoko said sadly.

"Me, too," Yui admitted then she reached out to pat the control panel, "but at least I'm going out in good company."

"Is the self destruct still off the table?" Naoko asked after a moment.

"It's too strong," Yui agreed, "too many people on the surface would die."

"Then I'll initiate a full purge of the Magi after the bombs seal off NERV and the bio-weapon deploys," Naoko said calmly, "even if they regain access eventually, they won't get any useful data."

Yui touched the control's again gently, "Thank you, and I'm sorry I have to ask you to do this."

"We both agreed this can't continue," Naoko agreed. She paused then noted quietly, "Fifteen minutes to detonation."


As the elevator raced to the surface Misato tried her phone, noting with some relief it was working. Dialing fast she listened to it ring, then as it was answered barked, "Ritsuko?"

Ritsuko gasped softly in relief as she said, "Thank goodness, I thought you were..."

"I'm on the express elevator out of NERV now," Misato said quietly, fighting off a surge of dizziness. "Did everyone make it out?" she demanded.

"The only unaccounted are you and Yui," Ritsuko answered quietly, "did you see her?"

Misato puffed out a sigh of relief, then shook her head as she felt a wave of pain from the back of her head. "It was Yui that triggered the alarms and the evacuation," she said after a moment, "she's plotting to destroy NERV."

"WHAT?" Ritsuko yelped.

"Can you get access to the Magi out there?" Misato asked as she leaned weakly against the side of the elevator, "We need to know what's going on..."

Upstairs in one of the evacuation gathering places Ritsuko and Maya Ibuki exchanged looks then Ritsuko answered, "Misato, I don't even have my laptop. Without some fairly sophisticated equipment I can't..."

Misato thumped her hand against the door as the elevator came to a stop, "Damn it."

The doors opened as Misato emerged in a area not far from Ritsuko and the others, and several NERV staff hurried to help her. "Ma'am, you're bleeding!" the young woman yelped at seeing the blood on Misato's head.

"Wondered why I had a headache," Misato muttered as she was bodily carried off, hurrying to a nurse treating minor injuries.

"Damn it. Boss!" Himiko yelped as they hauled Misato into the improvised command tent, "what happened?" The white haired secretary looked her over anxiously as she asked, "Are you all right?"

"I have a headache," Misato winced, "volume down, please."

Aoba Kinushima looked at her lover in alarm as the nurse looked Misato over. "Who did this?" Aoba asked flatly as the boyish brown haired woman clenched her fist, "I'll..."

"Yui," Misato answered. She looked over at Ritsuko and Maya, "Any luck?"

"No," Ritsuko admitted, "all I've been able to do is get a communications link open to the base, and Yui isn't answering."

As a nurse cleaned up the blood on the back of her head Misato asked Yui, "You can still get out, can't you? Please, Yui..."

"It's too late, now," Yui answered serenely, "there's less than five minutes."

"What are you doing, exactly?" Ritsuko pressed, knowing that someone had to ask.

"Well done," Yui murmured approvingly. "I'm using several bombs to seal off NERV," she said conversationally, "and detonating several medium duration bioweapons. They'll trigger the auto-seals, preventing any access for at least twenty years."

Maya Ibuki stood by her lover Ritsuko, the brown haired woman frowning. "That won't destroy the Evangelions or Archangel," she noted.

"I've taken steps to deal with those too," Yui said, "a tailored, flesh eating pathogen. With my death and the destruction of NERV's computers, the era of Evangelion will be over."

"And after twenty years?" Ritsuko asked, frowning.

"The majority of technology will be useless or seriously damaged," Yui answered, "but I would suggest keeping a eye on the facility, just in case."

"We will," Maya offered, looking up at Ritsuko who nodded seriously.

"Yui," the somewhat dazed Misato managed, "please don't. There has to be another way."

"Not for me," Yui said. Sadly she added, "When Rei and Asuka get out of the hospital, tell them... tell them I'm sorry, and I wish things could have been different."

"What about Shinji, Yui? You're condeming him to being in Unit-01 forever," Ritsuko asked.

Yui hesitated a moment then said regretfully, "He's practically immortal and will have the chance to explore the universe in a way no one else ever will. I hope someday he'll forgive me."

"Yui...," Aoba started quietly.

"Goodbye," Yui said and broke the connection.


Yui heard the explosions, listening as the bombs began to detonate in sequence in NERV, cutting off critical systems and closing off access tunnels. She clambered up over the terminals, looking down at the Magi computers down bellow.

"Copying my jump?" Naoko asked after a moment.

"The flesh eating bacteria will hit humans, too," Yui answered as the lab coat fluttered around her, "I don't want to experience that."

"I understand," Naoko said quietly. After a moment the computer added, "It was a honor working with you."

"You too," Yui said, letting go and allowing herself to drop.

There was a wet thud, then Naoko Akagi was alone in NERV. She felt a flash of regret at what she was about to do, but was comforted in knowing the staff of NERV would survive. As each segment of the Magi was erased she felt like a piece of her soul was fading away, then the final computer began to go...

"Yui?" Naoko blinked as a shining figure descended towards her.

"Not exactly," she smiled, "it's time to go."


Over the next few days the city fought to recover, both from the damage that Nao Rokubungi's suicide attack had done, as well as assessing what Yui had accomplished. The best technicians of NERV soon determined that their base was sealed tighter than a drum, and there seemed no possibility that the biological weapons could escape. NERV headquarters was sealed away for the near future, but the city would continue to thrive.

"So what now?" Asuka Soryu Langley asked as she sat up in her hospital bed, the redhead once more swathed in bandages.

"NERV has been officially shut down," Misato told her, "there will be a investigation, too. A lot of finger pointing etc etc, but I think we'll make it through all right."

Rei Ayanami sat by Asuka and took her hand, the pale girl frowning. "So the fighting is over?" she asked curiously.

"Yes," Misato smiled at her gently, adding mentally, 'for now at least. Who knows what tomorrow will bring?'

"Maybe we can take some time for ourselves," Asuka said, smiling slightly at Rei.

Rei squeezed her hand and smiled back, "I'd like that."


Notes: This is a 'flash forward' to Chapter 50, more or less. Since I decided to rewrite this fic I thought the readers deserved to see the planned ending. This also sets up plot points for my fanfic Bubblegum Crisis 2055: Megatokyo Burning which is a sequel to this fic.

My plot for the inbetween episodes was pretty simple: Hikaru starts training to use Unit-02, but before she can be certified the attack on Nao Rokubungi's base happens. NERV discovers that she launched her Unit-14 early, and that it & a stolen Evangelion carrier are on their way to NERV HQ. Hikari holds it off long enough for Archangel and Unit-0 to return, and a knock down brawl erupts. Nao and Mana attempt to detonate a N2 mine to kill themselves and the other Evangelions, but the combined AT fields of Unit-o, 2 and the Archangel stop her.

But in the chaos Yui Ikari decides enough is enough.

The rewrite I'm planing has the catchy title of 'Rebuild of Third Genesis' because hey, why not rip off the best? ^_~ About a third of the original chapters will be migrating over, more or less. I'll give more info as I get closer to releasing it...