A glass of water was placed on a coffee table in front of Shinji who was sitting on a couch. He looked up to see that was Hyuga who gave it to him. Shinji thanked him and Hyuga nodded in reply. He watched the man as he walked away to assist Ritsuko at the terminal. Shinji was confused by the fact that he didn't seem hostile to him, but he hadn't spoken a single word to Shinji since they met. He didn't know what to make of it.

After taking a sip of his water, Shinji made a closer look of the apartment he was in. The first thing he noticed was the cats. Not real cats, but cats that were in everyday objects: Pictures, pillows, hand towels, even a set of salt and pepper shakers on the kitchen table, a white cat for the salt and a black cat for the pepper. Otherwise, he found the apartment a rather simple affair. He concluded that it had to be that way for someone who could be gone for months at a time. Shinji moved the chair he was sitting in short jerky motions trying to expel the nervous energy he had, but to it was to no avail.

"Okay Shinji, we are ready," Ritsuko announced. Shinji brought his chair to a stop, a combination of relief and dread engulfing him. He knew he could stop, that he could walk out of the apartment, but the greater part of him knew it was worse not to know. Ritsuko took a breath before she spoke.

"Before I begin, I should point out two things. The first is that we were attempting to give you a variation of this briefing when you first came out of Unit 01. However, we were unexpectedly interrupted at that time, to say the least. The second is that this briefing will be neither comprehensive nor in a strict chronological order. While some general events will be mentioned, our focus here today will be on how your actions became a catalyst for the events in the intervening years. Do you understand?"

"I do," Shinji replied.

"Good," she said "Now, I want to begin by going back to the battle with the 10th angel. The lights were dimmed and a large monitor in front of him lighted up projecting a video of Unit 01 in battle. He watched as the Eva dragged the angel along the launch track. The screen switched to the Geofront, and he saw Unit 01 twisting the creature's arm before it just stopped.

"At this point, Unit 01 used up all of its battery power and shut down," Ritsuko stated. The screen showed the angel impaling it and casting it aside, the Eva spraying LCL. The video then stopped at that point. "Do you remember what happened next?" Shinji took a breath before answering her.

"I was hurt for the most part, I even spit out some blood. But I also felt very angry. I thought I'd failed in getting Ayanami. I wanted to make it give her back. I was going to make the angel give her back." Shinji realized that he had clenched his fists as he was talking, and he unclenched them, taking notice of the indentations made when he dug his fingernails into his palms. "Then the Eva started up again."

"Interesting…" she said. "This is what we saw on the outside." The video began to play again and Shinji saw Unit 01 reactivate, changing its color and growing an arm made of light. He saw it deflect the angel's counterattack and incapacitate the beast. He then saw Unit 01 stretch out its intact hand at the angel's core.

"Were you still aware of what was going on?" Ritsuko had stopped the video once again.

"I didn't see in the entry plug all of this," he replied. "Just a bunch of streaming colors, like a rainbow was all around you. And I don't know if I'm explaining this in a way you could understand, but there was something like an instinct or sixth sense telling me where the Angel was. And that same instinct was telling me to reach to Ayanami, that she was only a few meters away. Even when I heard her say that she couldn't be rescued, I was… compelled to save her."

"You heard her?" Hyuga asked looking surprised.

"I did," Shinji said. "I began to crawl towards where she was, and this is going to sound weird, but it felt to me that I was crawling farther than the length of the entry plug itself. I finally reached her and pulled her up, and holding her was the last thing I remember before waking up on the Wunder."

"I see," was all that Ritsuko said as she restarted the video. Shinji saw a massive vortex of radiating black and red bands form followed by the angel explode in a mass of blood, like all angels he'd fought before. But this time, the blood reconstituted itself into an image of Rei, almost as large as Unit 01 itself. He saw the image of Rei merge into the Eva and the Eva then beginning to glow, sprouting streams of colors, some of these streams forming into wings. Shinji always thought that Unit 01 was scary, but seeing like this, it looked completely hellish to him.

"Was this when it happened?" Shinji stood up. "Was this when the world was destroyed?"

"While this is Near Third Impact, it is not," Ritsuko replied. "You will see why any second now. Blink and you'll miss it." Shinji watched the screen and within seconds saw Unit 01 get skewered. He thought that the spear that impaled it look similar to the ones that were down in Central Dogma in the remnants of Lilith. He saw the the hole in the sky disappear and the Eva return to its normal colors, the glowing arm disappearing into thin air. The Eva floated back to the ground, the tip of the spear setting into the soil, leaving Unit 01 propped up in the air in an unnatural position.

"Who threw that spear?" Shinji asked, though the question wasn't directed at the other two in the room. The question was answered for him as he saw the Mark 6 descend from the sky. It was there too, in Central Dogma he realized.

"Eva Mark 6," he muttered. Ritsuko overheard him and replied.

"Correct. There is a lot to say about that Unit, but we would be getting ahead of ourselves. For the moment, it is sufficient to say," the screen now turned to a still picture of several people at one of the Eva cages where the Mark 6 was secured. The people were looking up at he pilot who had just left the entry plug. Ritsuko began to magnify the picture, focusing on the pilot. When the image of the pilot was made clear, Shinji's eyes widened at his identity as Ritsuko hammered in the point. "That the pilot was Kawrou Nagisa." Shinji stared out at the image for several seconds taking in all the implications of that revelation.

"Why?" he whispered, but still loud enough for the other two to hear it. "Why didn't he tell me?" If either Ritsuko or Hyuga were going to offer an answer, neither of them got the opportunity as the doorbell rang. Ritsuko walked over to the door and touched the pad next to it.

"Who is it?" she asked.

"Housekeeping," replied a masculine voice making an attempt to sound like a woman by raising the pitch of his voice, and convincing no one.

"I'm sorry, but I don't know-" She was interrupted by the door opening on her and seeing Burke standing in the entryway.

"Don't tell me you forgot that we're responsible for the security of this building?" Burke stated. "We can access people's doors in an emergency as well as feeds in the security cameras. You know, you can find some of the most interesting conversations that take place in the hallways." Ritsuko bit her lip before she spoke.

"Come on in, Vice Commander," her voice and actions stated to him it was the last thing she wanted to do. Burke walked in and looked upon the scene.

"Well, it seems I missed the cartoon, but made it in time for the main show," he declared as he took a grand look at the three who were there.

"Mind if I ask why are you doing this?" he asked. Hyuga looked at Ritsuko, while she in turn, looked at Burke with a steel glare.

"Fixing a mistake that you and the base's commander made," she told him. "We're attempting to rectify that."

"There are reasons for that," Burke said before sitting down next to Shinji. "Why did you ask her for this?"

"I needed to know. You did tell me some things. But not what was important."

"Because you weren't ready for what this all entails," Burke countered. "Besides, if you had some specific questions, you could have asked me. It wasn't as if I was going to bite your head off over it."

"I know," Shinji replied. "It's just that you were always so busy, I thought it would be a problem to bother you."

"That's not a bother," Burke stated. He planted his elbow on the table and laid his head on his hand taking a several deep breaths. He then lifted his head up and placed a hand on Shinji's shoulder.

"Look, I'm sorry that I haven't been around, and also that my actions made you feel that way. Do you understand?" Shinji nodded in reply. "Okay. Now, I have to ask. Do you want to continue with this?" Shinji looked at him.

"I do," he replied. Burke sighed.

"Let's hope that's the right decision," he said. "But if you ever want to stop at any point, just say so and we will." He shifted his eyes towards Ritsuko. "I'll make it happen."

"O…Okay," Shinji replied, a little unnerved at the change in Burke's tone of voice, even though it was not directed at him.

"If the two of you are done here, can you please shut the door?" Ritsuko asked, "or are you going to invite that tactical team in as well?" Both Shinji and Burke looked towards the doorway and saw the shadows of the team against the hallway wall.

"One moment please," Burke said as he got up and went to the doorway. He stuck his head out looking at the ten man team that was lined up against the wall.

"Standby," he whispered to the lead man who nodded his reply. Burke came back in and closed the door.

"That's taken care of," he said to Ritsuko as he sat back down. "You may proceed Dr. Akagi."

"Thank you," Ritsuko replied. "Now, to say at that point that we were in a bad situation would have been a massive understatement. Tokyo 3 was ruined, the top of the Geofront torn open, Central Dogma exposed, and of our Eva Units, one was destroyed, one heavily damaged, and one that could not be safely activated. You were absorbed into Unit 01, Asuka was incapacitated and Rei was considered dead. And the only functioning Eva was not under our command. A pretty bad situation indeed, but it was not all doom and gloom. It was fortunate for us that the MAGI was transferable and that we could work from a reserve command center. We also heard that the UN approved funding for not only the construction of more Eva Units, but for fully automated systems as well." Ritsuko displayed schematics for the various iterations of the Mark 4. "At that point, we could only hope that we could hold out until those Evas and their pilots would arrive. Are there any questions?"

"What exactly happened to me in Unit 01?" Shinji asked.

"Our theory at the time was that you reached a high level of synchronization well in excess of 100%. By our estimate, it was between three and four hundred percent. Due to that high rate, you lost you ego boundaries and ended up floating around in the entry plug in a disembodied state. The problem was that we weren't sure if you were still in the entry plug or if you were absorbed into Unit 01's control system. Even if we had little information to go on, we attempted an operation to salvage you out of there."

"And it didn't work," Shinji said.

"Correct," was her answer. "We don't know if it was because you were in the control system or if the control system refused to let you go. You do know about Unit 01's control system?" Shinji nodded yes.

"I know my mother is in there," he added. "Sub-Commander Fuyutsuki told me while I was at Nerv."

"Okay, that saves me some time," Ritsuko was tapping on her computer for a few seconds before she spoke again. "It could even be theorized that you, on a subconscious level, didn't want to come out. Tell me the truth, if you had the choice, with all that you had experienced, whether to leave Unit 01, would you?" Shinji hung his head low. He didn't want to look at any of them in the face.

"No," he replied.

"As I thought," Ritsuko stated. "In fact, that's what we had assumed. When we recovered Unit 01 from orbit, we were surprised when the data suggested that you were reforming in the entry plug. We had to scramble for the needed equipment to retrieve you. At the time though, we still had a few options to try to get you out, but we never got the chance." The screen then showed a video of a large mass of helicopters in the air above the Geofront. "The UN seized the Geofront and confined all Nerv personnel to an aircraft carrier."

"Makinami already told me that happened," Shinji said.

"Did she also tell you that Asuka was transferred to another facility?"

"N…No," Shinji replied. He was about to speak more, but Ritsuko cut him off.

"It was probably for the best, and it's not germaine to the briefing here. Another item worth mentioning before we move on was that both Commander Ikari and Sub-Commander Fuyutsuki evaded detention and disappeared, we didn't know where. It was likely that they were being sheltered by Seele."

"Seele?" Shinji asked. He thought he heard Asuka mentioned that name when they fought.

"Oh, you were never told about them while you were at Nerv?" Ritsuko asked. Shinji shook his head no. "I'll give you the short version then. They are the group backing Nerv. I can't give you many details about that group since the line between hard fact and rumor starts to blur when it comes to them. Suffice to say, they are not very good people."

"Now, it was during our confinement that Misato and I, along with Makinami and Burke here came to us. Shinji turned to Burke.

"You were with Kaji at that time?" he asked him.

"You bet," Burke replied. "Like Makinami, I was a pilot candidate as well."

"You?" Shinji looked at him with a mix of surprise and wonder.

"It's true," he continued, "but my experience was nothing more than a few physical training sessions, some sync tests. I never got a chance to get into an Eva. Makinami proved to be the more capable pilot. Do you want to tell you about the time she raced across the training facility wearing nothing but a towel because—"

"Vice-Commander, could we please get back to the matter at hand?" Ritsuko interrupted. Burke gave her a quick glare before nodding.

"Thank you," she said before continuing. "It turned out that the three were part of the UN not affiliated with any Evangelion organizations. It turned out that their group was in opposition to Nerv and presented us with information that gave us a rough idea of the Human Instrumentality Project. Long story short, he recruited us into what we know now as Wille. At the time, we were still officially affiliated with Nerv and we would have to remain on the carrier for the time being. However, we would soon get our chance to do something about it."

"What do you mean?" Shinji asked.

"The 11th angel," she replied. "The people who took over from us at HQ were a competent group, I'll give them that." She began displaying images of tanks in formation, helicopters on patrol, and defensives being erected. "With the Mark 6 backing them up, they were more than confident that they could beat back any monstrosity that came at them. "She then showed an image of the inside of a tent containing rows of cots, all of them occupied by a bedridden person.

"They all had the same symptoms when they were first brought in: Headaches, dizziness, blurry vision, bleeding from the eyes and nose on some of them. When a medical scan was completed on some of the patients, it showed that there were large clusters of bacteria settling on portions of their brains. Further analysis returned blood type blue. Not only were people becoming infected and some of them even dying, some of them were exhibiting odd behaviors." The screen played a video montage of various men and women repeatedly walking into a wall, going in circles, setting up and putting away tables and chairs ad infinitum. "It can only be assumed the bacteria was learning."

"Learning?" Shinji didn't understand what she meant. Ritsuko tapped a few keys on her laptop and brought up an image of a human brain with blue patches on it.

"Apparently, those clusters weren't just settling on random parts of an infected person's brain. Placing scans from multiple patients side by side showed the clusters were on the same areas, or at least very close to them. These are areas that control movement, balance, and memory. Furthermore, the clusters were able to send and receive signals to each other similar to human nervous system. And all of these factors led to this." She brought up a video showing two soldiers standing guard when they were approached by a third that seemed to be walking unsteady. There was no audio, but Shinji could tell that the guards began to talk to the third, who offered no response. After a minute, the confused guards approached the third, who then shot the other two. The screen switched then to another video of two soldiers shooting up a full canteen, followed by another video of someone trying to trying to strangle a nurse in the medical tent. Shinji turned his head away, he couldn't watch anymore.

"You can see that it was quite the situation," Ritsuko resumed speaking, "They tried to control the situation but it kept getting worse. Reaction led to overreaction, and everything went straight to hell." She then showed a video of the area around the Nerv Pyramid in flames accompanied by a chorus of explosions.

"How did you deal with it?" Shinji asked.

"Well, it wasn't easy," Ritsuko replied. "I mean, what do you do when using an Eva is unfeasible? And to compound our problem, antibiotics didn't work and nanomachines injected into patients were repulsed by the clusters using an AT Field. The first thing we had to do was to contain the infected people so that they wouldn't make contact with Lilith." She then brought up a still image of several large black columns being set into place. "These are anti-angel hex pillars. They're designed to neutralize an angel's abilities. We found when they were set up that any infected person would stop their advance. They weren't cured mind you, but they did see a reduction of symptoms. The next stage was figuring a way to defeat the angel. The best way we thought of was to engineer a virus to attack it without harming the patient. Deployed via aerosol, we were able to eliminate all traces of the angel within a month. The angel was defeated, but that was not our only purpose there. As members of Wille, which was still a shadow organization at this point, we had a secondary mission that ran parallel to defeating the angel. The first part of that mission was to get the MAGI away from Nerv and Seele control. We secretly transferred the OS into an identical structure halfway around the world while making it look as if it remained at Nerv HQ. I think it was one of the most clever things I was ever a part of, if I do say so myself." She beamed at that last sentence as Shinji looked confused and Burke rolled his eyes. She continued on.

"The second part was that under the guise of checking on the Nerv personnel still confined, Misato led a raid on the facility Shinkinami was being kept,and retrieved her."

"Was she okay?" Shinji asked. Ritsuko paused before she answered.

"It… might be best to ask her," she told him. Shinji slunk in his chair. He knew that would go nowhere remembering that she told him that it was none of his business when he asked her eye. He wondered if the two were related, but there was no time to ponder it further as Ritsuko continued to speak.

"The third part was to gain access to both Unit 01 and Unit 02. The latter unit was easy to get at, but we were unable to get to the former. After the 11th angel's defeat, we did receive some interesting news from the people who were holding it." The screen showed a new image and Shinji saw… himself in that picture. The hair was a little longer than he would normally keep it, so he couldn't see the doppelganger's eyes, but it did look like him. Shinji stood up in amazement at what he was seeing.

"Is that…me?" he asked.

"We thought it was," Ritsuko replied. "Captain Katsuragi… she was so glad when she thought that you had been recovered. She broke down and cried right in front of…well, I can't say you, can I. The DNA from it matched the records we had of you. It had no memory of what happened before, but that was chalked up to any trauma from being absorbed into and being reconstituted from Unit 01." She paused again for a few moments before speaking again. Shinji also noticed that both Hyuga and Burke had their heads down.

"One day, it suddenly attacked us, and it…maybe it's best to show you." The screen then displayed a video of several people shooting at something off screen. In a flash, the doppelganger charged at them with super human speed, and ripped through the defenders, tearing them to shreds. Shinji sat back in his chair and doubled over below the table, holding his hand over his mouth. The nauseousness soon went away, but he couldn't shake the image from his mind. "We refer to this creature as BM-01," she added.

"I feel sorry for the bastards who had to clean that mess up," He heard Burke mutter to himself. He felt a hand on his left shoulder, and when he turned in that direction, discovered Hyuga squatting next to him.

"You're going to be all right?" he asked Shinji, who nodded and waved him off. Hyuga returned to his seat, though he kept one eye on Shinji.

"There were forty of us who came from the carrier to fight the angel. Only seven of us remained. Misato… it took her a while to recover from it. I'm not even sure she has." Ritsuko murmured those last words. Shinji then spoke up.

"If I was still in Unit 01, what exactly was that…thing?"

"We're getting a little ahead of ourselves," she replied. "I want to discuss with you a few more pertinent facts before we get there." She brought up another video, this time of the 12th angel, twisting its way towards the ruins of the Geofront, receiving long-range fire from its defenders. "The 12th angel attacked. Naturally, the Mark 6 was dispatched to engage it."

"Kawrou fought the angel?" Shinji asked.

"No," She replied. "It was outfitted with an improved version of the dummy plug designed to allow the Eva to react to unforeseen situations." The video continued showing the Eva deploying against the angel, the two monstrosities barreling towards each other. The Eva then stopped in its tracks, the center parts of its torso blew off revealing a core, and spread out its arms as if was going to receive a hug. The angel hit the Eva's At Field, and at first seemed to repulse it. However, the angel pierced it, but it was more like a the Eva let it through, entering the core. After the angel was absorbed, the Eva appeared to pulse for a few seconds before it grew in size and and some of the colors began to turn to a sinister red. The Eva began to walk in a lumbering fashion towards the remnants of the pyramid.

"Wh-Why did it absorb the angel?" Shinji asked. The video continued to play showing the Eva now floating down the main shaft towards Lilith.

"There are two distinct reasons," Ritsuko answered. "The first is that we found out afterwords that the dummy plug had unique programming in it to make the Eva do just that." The video continued to play, the Eva had now breached Lilith's chamber. The tank battalion an a squad of VTOL craft were throwing everything they got at it, though it was to no avail. The Eva got closer to Lilith knocking the tanks and aircraft away with one of the craft landing on where the camera was filming, resulting in static.

"The second reason was that there was a…foreign body in the plug," she continued.

"Foreign body? I don't know what you mean." A sickening feeling was beginning to grow in Shinji's stomach.

"Another you, whom we refer to as BM-02," she stated. "Same genetic profile, same everything. All they had to do was place the thing in the plug."

"But why would they need…me to be in there?" Shinji asked. Ritsuko took a breath before she spoke.

"After 3rd Impact, Misato and I were sent as part of an investigative team into the epicenter. We found the video you just saw along with one individual of whom we did not expect." The monitors then showed a still picture of a group of people surrounding Kawrou Nagisa.

"Kawrou!" Shinji yelled.

"It caught us as much off guard as it did you," She remarked. He gave us some details of 3rd Impact we did not know along with a few revelations. The first of these was the existence of the Ayanami types." The screen showed a picture of several Ayanamis in LCL tubes.

"The second was that Nagisa was similar to Ayanami, that he was a clone, and he was the first angel." Shinji did remember him rambling something about being cast down to the 13th angel, though he didn't know exactly what he meant.

"The third was that there were clones of you as well." The main screen was filled with a large image of multiple Shinjis in a large tank of LCL. Shinji stared at the image not saying a word. The bottom half of his mouth quivered as he if wanted to say something, but no words came out.

"According to Nagisa, there were several of them that were around as children and he interacted with them. He even considered one of them a good friend," she continued. "Based on the actions of BM-01 & 02, you should now understand why you received the reception that you did aboard the Wunder. There was no way to immediately tell if it was really you, or if you were another copy ready to kill all of us. It could have been another trick courtesy of Commander Ikari."

"H-How were you able to tell if it was really me?" Shinji's voice was beginning to grow unsteady, and Burke took notice of it.

"We were able to take blood samples that we had sent here to New Constaninople to see if there were any signs of particular chemicals in your blood stream. The copies, like the Ayanami types, require these chemicals in order to maintain cellular cohesion in their bodies. This is due them being grown in a lab while you were carried by your mother, so you don't have that condition. However, there were some unique circumstances found when we analyzed samples from the copies."

"Samples?" Shinji's voice now sounded distant to Burke, as if he wasn't entirely there.

"Dr, Akagi, perhaps it's best to call it a day," he said. "What he has been told today is a lot to take in." Ritsuko answered Shinji.

"When we completed a more in depth analysis of your genetic structure, we discovered two things. The first is that there is no genetic connection between you and Gendo Ikari."

"He..He's not my father?" Everyone in that room could see the glint from tears forming in his eyes.

"No he is not," she replied. She was about to say more when Burke interrupted her.

"Vice-Captain, I insist that you cease with this briefing immediately. Can't you see that he needs time to process what he as already been told?"

"Maybe we should stop," Hyuga added. She ignored them both.

"The second discovery is that while your genetic makeup is mostly that of Yui Ikari, we found that there is angelic DNA within you and the clones that were based off of you."

"What does that…" Shinji didn't finish the question.

"It's means that you are not a true human being," she answered in an eerily calm demeanor. "You now know the truth. The question is whether or not it sets you free." In less than a second, Ritsuko was facing the business end of Burke's pistol.

"Do you know what the hell you've done?" Burke's voice was a sharpened knife.

"I told him what he wanted to know," She replied. "That's all I did."

"Did you have to be so damn specific with the details," he said. "I understand telling about the clones, you didn't have to tell he wasn't human, at least not now."

"Then when?" she countered. "Next month? Next year? Two or three years?" Burke gave no answer, and Ritsuko gave a thin smile. "I saved you all the trouble."

"But the cost you damn woman," Burke spat out. "You have to think of the cost. You didn't think of that, or worse, you decided not to. Which is it?" Before she could give an answer, Hyuga, who had been holding his hands up ever since Burke pulled out his gun, spoke up.

"You guys do realize Shinji left already." The two turned their heads towards where he was sitting, finding no one there. Burke rushed to the door and peered out into the hallway. He saw the tactical team that he had left, but Shinji was nowhere in sight.

"Where did he go?" He asked the team leader.

"That way sir," he pointed right behind him. "It's weird sir. The kid acted really out of it. I tried to say something as he passed by, but it was like he didn't hear me."

"Sweep the building for him and get me in contact with HQ. He needs to be found now."