Note to self: stop writing Adaptation for a week or so and work on other stuff.

Adaptation

Scenario 1: The Looming Darkness

Lieutenant General Shinji Ikari of the United States Army was not a happy man right now. His vacation had just been cut short, and it was a vacation that he had needed. Besides, he was enjoying the time with Asuka and Jessica. After all the losses he had had to suffer in the few months, he was ready to get back to life and enjoy what was left of it.

"I hope this is important," he said to the Joint Chiefs of Staff.

"Major, play the sequence."

The major pressed the button on the remote and the hologram activated. It showed a blob of black matter that started killing everyone around it. After a few minutes, it destroyed the camera. The generals then looked at him.

"What was that?" he asked them.

"We were hoping you could tell us," General of the Air Force Charles Heinz replied, "This was recovered from one of the salvage sites. Currently we have no other data, except that one of the soldiers was stripped of her clothes."

"Hmm. Perhaps something survived from the Ark," said Shinji.

"That would be pretty obvious," said General of the Army Ralph Winters.

"What is even more disturbing is that two other sites have also failed to report in," said Fleet Admiral Wyatt Peterson.

Shinji let a small smile appear on his face.

"Then we are faced with a rather interesting situation," he said, "The only question that remains is what the Joint Chiefs will do."

"We are considering activating Project MATRIX."

Shinji raised an eyebrow. That project had been proposed after the Pentagon had received data regarding human evolution from Shinji. That data had been collected by NERV and had most likely fueled the ambition to get Noah's Ark.

"And how exactly am I involved?" Shinji asked them.

"We would like you to head this project," said Heinz, "The primary problem we have is that none of our troops know how to deal with Angels. You on the other hand have killed many of them by yourself, and you are also an EVA pilot. A decided advantage."

"True. So, where will MATRIX be based?"

"We will be taking over the NERV complex," said Winters, "If you so wish it, you may retain the former NERV staff."

"What about Commander Katsuragi?"

"I doubt the president will authorize it," said Peterson, "US troops will provide security, and you will still have the troops around Tokyo 4 at your disposal."

"Hmm. Very well. However, I do have one request. I will need access to Gendo Ikari and Misato Katsuragi. As both were commanders of NERV, they may have information to assist us."

"Is it likely that they will cooperate?" Peterson asked.

"Gendo will most likely cooperate if he is allowed to meet my mother once."

"We will consider it," said Heinz, "There are some political issues, but hopefully we can get around them."

"Of course. Politics rarely doesn't affect something."

"True. Now General Ikari, will you take this position?"

"Of course. The Angels are still a threat to humanity. However, these second generation Angels may very well be capable of destroying humanity this time."

"True. When can you leave for Tokyo 4?" Winters asked.

"Two hours. Will my daughter be joining me again?"

"If you wish it."

++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

Asuka and Jessica were waiting outside, Jessica playing with her blond hair as Asuka watched the girl fondly. Once she had felt jealous that Shinji had opened up to someone else besides his Japanese family, but now she understood. Jessica was like them in a way. She wasn't exactly sure how Jessica was able to pilot an EVA, but maybe Shinji knew. Just as the thought crossed her mind Shinji walked out of the conference room. Asuka and Jessica both immediately stood up.

"So?" she asked.

"I'm being sent back to Japan," he replied.

"But they promised you would get some time on leave!" Asuka said.

"I can't help it. But if the two of you don't want to come along, I understand."

Asuka flicked him lightly on his forehead.

"Idiot. Of course I'm coming with you, and so is Jessica. Right?"

Jessica nodded frantically.

"Fine. Let's get our stuff them. We're leaving in two hours."

"What!"

"Now aren't you glad I told you not to unpack?" Shinji said to her with a smile.

Asuka gave him an annoyed look but walked with him. Shinji took Jessica's hand and the three left the main office wing. They returned to the room where they had dumped their clothes and quickly got them. A Humvee was waiting for them outside and the three got in. They would be taken to Andrews Air Force base and would take a plane from there. Hopefully it was one of the new Concordes. Those planes were extremely fast and comfortable too.

++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

Hikari and Toji were rather surprised by the summons. What surprised them even more was that the rest of the bridge crew excluding Asuka were also present. Before them sat several very high ranking American officers.

"I'm sure you're wondering why you have been summoned," the general in the middle said, "The primary reason you are here is because we need your services. NERV is being reactivated by the UN because of a new emergency that has arisen. I am here to ask you if you wish to return to Japan and work under General Ikari."

"What exactly is this new threat?" Kensuke asked.

"We are not completely sure," said the general on the right, "but we believe that some things survived the Ark's destruction. They may very well be trying to end humanity again, just like the Angels did during the year 2015."

"And you are asking us to rejoin NERV," said Toji.

"Yes. Our current situation is extremely delicate and the primary problem we have now is that there are few people experienced in dealing with Angels. Most of them are dead, because of the attack NERV suffered by the SSDF's Special Forces."

"And Shinji is going to be put in charge," Kensuke said.

"Of course."

"Then count me out."

The others gave him a surprised look.

"Shinji's been out of NERV for too long. NERV is not an American organization and I will not serve under an American."

"Ken, Shinji is Japanese!" Hikari said.

"Really? I never recalled that a Japanese citizen could be a lieutenant general. The man that we saw is not Shinji Ikari. He is Sam Richards, and I don't know him."

"Very well. Then please leave, Mr. Aida."

"Gladly."

Kensuke stormed out of the room. Hikari moved to follow, but Toji caught her hand and shook his head. He wasn't sure why Kensuke was acting that way, but it wasn't right to try to interfere.

"As for the rest of you, do you accept our terms?"

"Hold on," said Toji, "How big a danger are these creatures, and why are we being sent back to the NERV installation?"

"Because it's convenient," the American general answered, "The NERV installation offers us a base of operations, and because many of the fragments have scattered in Asia, Japan offers a nice place to launch operations from."

"What are the Angels after this time?" Makoto asked, "Last time they were after Adam."

"Again, we don't know," said the officer on the left, "The primary problem is that we know absolutely nothing about these new Angels. If we did, we would have done everything in our power to keep them away from it. Unfortunately, we can't."

The gathered NERV officers looked at one another and finally centered their gaze on Toji. He returned the looks and finally nodded to the US officers.

"Not like we have anything more important than saving the world," he joked.

++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

Shinji entered the room and looked through the glass wall. Misato Katsuragi and Gendo Ikari were being held in the same facility on Alcatraz Island. If it wasn't such a bad place to be, it might have been considered an honor to warrant such security. Their rooms were comfortable enough, but not luxuries. Shinji tapped on the glass and Misato looked over at him. She walked over and stared at him through the glass.

"So what brings you here?" she asked.

"Business. Your little plan with bringing the Ark to Earth caused some side effects."

"Oh? And how would I know about them?"

"Don't play dumb, Misato," Shinji snapped, "Do you have any idea how many strings I had to pull to ensure that you didn't get the death sentence?"

"So why did the prosecution ask for it?"

"Because that's what some people in the military and government wanted. I called in some favors and got you your life. Be grateful for that."

"That's about all I have to be grateful for," said Misato, "My son leaves me and comes back to wreck everything I worked for, and I lose my chance to get Kaji back."

"It wouldn't have been Kaji. Better to not live than live a lie. That's something you taught me, and I'm surprised you went back on it."

Misato let a smile appear. "So what do you really want?"

"NERV is being reactivated and I've been placed in charge," Shinji answered, "Is there any other surprises you haven't told me about?"

"A few. The only question is, why do you expect me to tell you?"

Shinji placed a hand on the glass and looked intently into Misato's eyes.

"Because I'm the closest thing you have to family, and I've already died in order to keep you from doing something stupid, like initiating another Second Impact."

Misato crossed her arms and chuckled.

"Shinji, you truly are an amazing individual. Very well, I'll tell you. There is one other project that the UN or the US isn't aware of. It was started by your father and is still running."

"What is it?"

"It's a prototype weapon, designed to help humans destroy Angels. After the Second Impact occurred, a massive burst of radiation was detected all around the world. It affected certain unborn children, causing them to mutate. Of course, all of the EVA pilots are such humans. Advanced humans. This concept would have scared Seele so Ikari hid the data. After a little while, he started developing equipment that would allow the children that were affected to access their full potential, to manipulate their AT-Fields.

"So where is it located?" Shinji asked.

"I don't know," Misato admitted, "However, there's more. This weapon was never fully developed, as Ikari didn't have any human that could access their AT-Field. Rei was the closest he got so it was only partially developed. If there was a human that could access their AT-Field, then an examination of their brainwave pattern would reveal how they were doing it. Also, a sample of their DNA would be able to finish the puzzle."

Shinji considered the information. He then nodded.

"Thank you Misato. Perhaps next time I come to visit it will be for more pleasant things."

"Perhaps."

Misato turned away and Shinji started to leave. However, at the door he stopped.

"Misato, what exactly are you after?"

"Forgiveness," Misato answered.

"I can never forgive the action of killing my friends," Shinji replied, "but I can forgive you. Oh, one more thing. What is this weapons project called?"

"Project 2E," Misato replied, "Second Evolution."

Shinji walked out of the room. He had one more stop before leaving for Tokyo 4.

The security around Gendo Ikari was even more tight. Shinji passed through five checkpoints before being finally admitted into the room. Again there was a glass wall showing into Gendo's room. Gendo saw his son come in and washed off the shaving cream. He turned to face his son. Shinji had grown greatly since the last time the two had met. He was now a man and had a dangerous look in his eye, a look that Gendo recognized as his own.

"Hello Father."

"Shinji."

"Watch the news?" Shinji asked.

"Of course. Two government scientists recovered."

"Kyoko Soryu and Yui Ikari, from Units 02 and 01 respectively."

Gendo regarded his son with care. The Shinji he knew was gone. A more confident and powerful one had taken his place. In a way, Gendo felt proud. His son was following in his footsteps, even if he didn't know it.

"And why are you here?" Gendo asked his son.

"I need the location of Project 2E."

Gendo considered the request.

"Why should I disclose the location?"

"Do you wish to see mom?" Shinji asked.

"Of course. So in exchange for information, I'll be allowed to see Yui."

"Yes."

"How many times?"

"That will be determined by her. I cannot force Mother to do anything she doesn't want to."

"Understandable, but what are you going to do now?"

"Win. The scenario that I planned will succeed, unlike yours."

Shinji's eyes started glowing red and his white became white. A grin appeared on his face as he looked at his father. A few seconds later he returned to normal.

"As you see, the prototype is ready for use by humans. I'm proof of that."

"Indeed you are. Very well, I will supply you with the location of the prototype. However, I doubt you will be able to utilize it until this is over."

"Don't be so sure, Father. The only reason that I even asked for the location is that I know how to utilize it. Never underestimate your own son. I made the mistake of underestimating you at times."

Shinji let out a laugh, and for the first time in a very long while Gendo Ikari felt fear. That was not Shinji's laugh. No, it was that of someone else. His friends were blind to not have seen this. If they wanted to save Shinji, they would have to act fast. However, no one would believe him. The only hope the planet had was that Shinji make a mistake, though if that happened it would probably be too late.

++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

"Lieutenant General Shinji Ikari."

Kensuke muttered that name as he considered the facts. Facts, not rumors or beliefs, or any other nonsense.

"So what have you dug up?"

Kensuke leaned back into his chair as the other man walked in.

"What took you so long to get here?" Kensuke asked.

"The FBI keeps tabs on you and the others. They're a lot more effective than I remembered."

"Perhaps. However, perhaps you can explain to me why you're sitting idle?"

"Because you're here. If you return to NERV, you may be able to find out what the facts are."

"You serve truth," said Kensuke, "I admire that. However, have you ever considered serving protection?"

"Protection. The only way I can protect them is with the facts. So, are you going to return to NERV?"

"No. Like you, I've prepared assets. I will do what I can, from the outside. It's surprising how much freedom you have if others don't think you're interfering."

"Let's hope this works."

"You should have been able to prevent this. Are you going to fix your mistakes, Kaji Ryoji?"

Kaji smiled. After so many years, the Angel War would be starting all over again. It had never ended, because the First, Second, and Eighteenth Angels were never defeated. But it was more than that. Humanity was on the verge of becoming even more powerful than any Angel. However, again someone was preparing to manipulate that power. Misato Katsuragi had not understood what she was doing, but the new commander did. There was a big difference between blundering in the dark and walking a lit path. Kaji knew he would hate himself for what he was about to initiate, but if he didn't do this, something worse than Third Impact could happen.

++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

The US Concorde flew into the US Command Base outside of Tokyo 4. The US had considered downsizing the forces stationed in Japan, but with the new Angels scattered all over Asia, that idea had been scrapped. Chinese forces were also activating several reserve divisions and preparing to face this new threat. Shinji had sent in a set of parameters for the MAGI to look over to find other people like the EVA pilots. So far, only three others had been found. With all of the living EVA pilots and Hikari, that only made eight. They were being sent to Tokyo 4 as NERV was being reactivated. That name had give hope to many, driven fear into others, and would now may just redeem its name.

"When you arrive at the NERV complex, make sure the American techs didn't screw anything up," Shinji said to Asuka, "I'll join you after I take care of something."

"Where are you going?" Asuka asked.

Jessica also gave her father a worried look.

"Don't worry," Shinji assured them, "I'm just going to retrieve something. After that, I'll return to Tokyo 4. Besides, there are still a lot of things the US needs to take care of before NERV is fully active again."

Shinji closed his eyes as the plane started to descend. Adam had been quiet of lately, and Shinji wasn't sure why. He tried contacting his other self again.

Adam. Are you there?

-Where else would I be?- was the Angel's sarcastic reply.

Shinji smiled inside, slightly surprised that the Angel could display emotions.

There are a few more things we need to talk about.

-Of course. I would assume that how do defeat the new Angels would be one of them?-

That would be one of the more important topics.

-These Angels have no cores, unlike the EVAs and past Angels you have defeated. Unlike you or me.-

Of course.

Unknown to anyone else but Shinji and Adam, an S2 organ had replaced Shinji's stomach and much of his digestive system. A core had also taken the place of his heart.

-However, they do have an S2 organ, and have the ability to cause a disaster very much like what happened to the NERV Second Branch in America. The only way to defeat them is to destroy or disable their S2 organ. After that, they're just as vulnerable as you lilliums.

And what are we supposed to do then, kill defenseless sentient beings?

-That is not my choice. Such a decision would fall under your jurisdiction. However, if you choose to keep them alive, understand this. They will not be loyal to you. They are loyal to me.-

And how am I to get them to become loyal to me?

-I do not know. If you are able to figure it out, that would be most impressive. Until you do, living Angels will still be a danger.-

When weren't Angels a danger to humanity? Shinji asked Adam.

When you lilliums finally learn to accept peace within yourself.

Shinji couldn't help but laugh aloud, drawing the attention of Asuka and Jessica. Both gave him looks as if they were in the presence of someone not completely sane. Shinji ignored the looks and looked ahead.

Humanity will never do that, he said to Adam.

-I know. That is why Angels and you lilliums will always fight, for eternity.-

Until one wins, or we destroy each other.

-If you lillium win, that will be the true miracle.-

Shinji nodded and waited. The Concorde landed on the runway and parked. Asuka and Jessica got off, but Shinji remained onboard. After refueling, the Concorde took off again for Old Tokyo.

++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

Asuka led Jessica through the base to their rooms. Their bags had already been dropped off and the two started unpacking.

"Does Shinji travel around a lot?" Asuka asked.

"Dad does have to go away sometimes for missions. According to him the US has some problems with extremist organizations in the south, so Delta Force gets called in to handle them."

"Ah. Can you tell me about Sarah?"

Jessica nodded sadly. "She and Dad were really close. They met in training and Dad tried to not involve himself with women at the time, or that's what other people told me. But Sarah was like him a lot. People both said they had a past they wanted to put behind them. That's why they started dating. But after a little while they had to stop because Dad got promoted and they were swamped with work."

"Did you like her?"

"She was like a mother to me. I really liked her, and she was really kind. She always tried to look out for me."

Tears started streaking down Jessica's face. Asuka walked over and held the girl.

"I'm sorry I have to make you remember," Asuka said to her.

"No, it's okay. I want to remember."

"Dr. Soryu?"

A sergeant's head poked into the room. Asuka let Jessica go and faced the soldier.

"What is it?"

"The others are here. Do you want to talk to them now?"

"Others?" said Asuka.

"Yes, the former NERV officers that agreed to return to Tokyo 4 and serve under General Ikari."

"Oh! Sure. Jessica, come on."

The two followed the sergeant to a conference room. Inside everyone was gathered, including Kyoko and Yui. Asuka sat down at the head of the table and Jessica sat down to the right of her.

"Hi everyone," Asuka greeted, "So, who's second in command?"

Everyone looks at her.

"What?"

"Umm, Asuka, according to this, you are," Hikari said, holding up a pamphlet.

Asuka narrowed her eyes and then snatched the pamphlet. After flipping through it quickly she slammed it down on the table.

"You know, Shinji could have given me a bit more warning than just dumping me into this job," she said.

"Since Kensuke doesn't want to rejoin NERV Shinji probably thought you would be the next best," said Toji, "though I'm not sure why."

"Toji, remember who your superior officer is," Asuka said sourly.

Toji shrugged at the statement.

"All right. Since I'm in charge until Shinji's back, what exactly are we supposed to be doing?"

"You mean you haven't gotten your briefing yet?" said Maya.

"What briefing?"

A colonel suddenly walked in and gave Asuka a large envelope.

"You left this back in the States," he said before leaving.

Asuka's face turned bright red. She hadn't thought it was anything important.

"Am I supposed to be here?" Jessica asked.

"Sure, why not? You'll probably be hearing me complain about work, so it isn't like you won't find out anyways."

A few chuckles could be heard from the gathered officers. Asuka ripped open the file and started reading.

"Hmm. Okay. Apparently the first thing we're supposed to do is give the MAGI a complete checkup and make sure there are no holes in it. Shinji's worried someone might be able to find a way through the firewall."

"That would be very difficult," said Maya, "I mean, the entire thing is designed to keep people out."

"Doesn't mean there isn't a way in," said Shigeru, "Seele managed to find one, as did one of the Angels. And again Commander Katsuragi did."

Asuka took a deep breath. This was going to be tedious work. The original MAGI weren't as advanced as the ones in Germany, Russia, China, and the US. However, the MAGI NERV had was unique in its own way. Over the years, its capabilities had actually grown by itself and now it was more powerful than the others. If the other MAGIs tried hacking in again, they would be in for a shock.

"So let's get to work. Oh, did most of us keep the same jobs?" Asuka asked them.

"I've been placed in charge of the Science Department," said Maya, "Hikari is in charge of the Engineering Department."

"I'm still head of Section 2," said Toji, "Besides that, I think everything is about the same."

"Okay. Shall we get to work?"

++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

Shinji was on board a command hovercraft while the SEAL team advanced towards the abandoned SSDF base. The soldiers were wearing green camouflage armor and they were almost invisible against the grass. However, the infrared scopes on the hovercraft easily picked them up. Unfortunately, that also meant anyone with infrared equipment could also detect the soldiers. Army Research was still working on a way to eliminate the heat from the stealth package, but so far had been unsuccessful.

"Red team reporting," a voice cracked over the radio, "We're detecting no resistance so far. Proceeding."

The US forces had surrounded what apparently was a former NERV lab. However, it was run under the dummy corporation Infinity. Shinji watched as the troops blasted open one of the doors. They charged into the building. Shinji watched everything through one of the headset video cameras. The SEALs found dozens of scientists working inside the large complex, and many guards. The Japanese guards tried to fight back but the SEALs were far more professional. They were also equipped with tranquilizer rounds as Shinji didn't want a bloodbath on his hands. After fifteen minutes of rather intense fighting, the US forces gained control of the complex.

"Have you found the lab?" Shinji asked.

"Affirmative. We've unlocked it. Proceeding in."

Several soldiers charged into the room, their rifles at the ready. They found nothing inside except for what looked like rather bulky body armor.

"Target confirmed. Shall we move it?"

"Not yet," said Shinji, "Secure the area around it and make sure nothing gets through."

"Roger. Wait, something's here. Fuck! Switch to shredder rounds!"

Shinji could hear live ammo going off in the room and thought he saw something slice through the soldiers. A second later, the camera was destroyed.

"Fuck. Sergeant, lock down that area and get all non-combatants out. I'm going in."

"General! That's no place for you to be!"

"If that's what I think it is, I may be the only person that can defeat it. Major, get me some armor and weapons."

End of Scenario 1

As a writer, I just write what comes to my head. I usually have an idea of what I'm trying to accomplish, but the fact is I write how I feel. I don't always have a plan. Anyways, besides that, please read Duet of Truth and Project: Omega, also by me. I think many of you will enjoy Duet of Truth. Hopefully I'll get around to updating it sometime.

Z98