Misato was interrogating the clone of Shinji's cousin, now identified as "Rei Q" or "Tentative name: Rei Ayanami". Ritsuko on the other hand was monitoring her vitals on her silver laptop sitting at a desk built in to the side wall of the cell. All three of them were in a room similar to that of Shinji's, except the clone was restrained to a chair that was also used in a dental clinic by the wrists, ankles, and chest. Various probes were attached to her to determine her bodily responses to certain questions. The clone herself was wearing the same jumpsuit as Shinji as she sat restrained and reclined in the chair.
"What was your purpose for serving Gendo Ikari and NERV?" Misato asked.
"My purpose was to function as a pilot for Mech-Fighter Unit-09 for the Commander, obeying orders and functioning as a commanding officer for the Command Operations Division." the clone replied.
"What do you mean by Command Operations Division?" the Colonel asked.
"It is an elite unit within NERV, only under the direct control of Commander Ikari and Deputy Commander Fuyutsuki." Rei Q answered." We are responsible for the direct implementation of the Human Instrumentality Project. We were programmed to only follow the orders of Commander Ikari and Chairman Lorenz. Our objective is to finish what we started 15 years ago."
Misato and Ritsuko were both puzzled and surprised by her last sentence. The Colonel then leaned in towards Rei Q, staring deep in to her eyes.
"What do you mean 'to finish what you started 15 years ago'?"
"Commander Ikari ordered a clone of Pilot Nagisa and myself to descend in to Terminal Dogma with our Mechanized Combat Aircraft to re-activate the Super Computer MAGI System and merge it with the thought patterns contain within Unit-6." The young pilot explained.
"And what was so special about Unit-06?" Misato questioned.
"Unit-06 contained a thought program in its brain known as the Tree of Life. The MAGI itself was installed with a program known as the Fruit of Life. We were tasked with dismantling Unit-06 in order to extract the program and install it in to the MAGI. Upon installation, the MAGI would the ecological event known as Third Impact, the first phase of the Human Instrumentality Project."
"That makes no sense, I saw the event my own eyes." Misato shot back at Rei Q. "Unit-01 and its pilot destroyed the surrounding area with unnatural powers they gained and in the aftermath."
"While Pilot Ikari certainly caused damage after the individual I was derived from was wounded, he only succeeded in destroying the GeoFront and the surrounding Third City of Tokyo." the young girl explained. "The city itself was mostly evacuated due to the ensuing battle. The commander had anticipated this would happen and used the following event to test if Unit-01, which contained both the Tree of Life and Fruit of Life programs, would enter 'Scorched-Earth Attack Mode'. If his theory was successful, he would duplicate the process on a much larger scale by having Unit-06 insert it in to the MAGI and initiate a proper Third Impact. We then released an official report saying that this was the side effect of Unit-01's pilot engaging Scorched-Earth Attack Mode. After that, the original plan was to have him placed in stasis in an unidentified area for later use, however Pilot Ikari disappeared shortly after."
"Within a few months of the Directly Supervised Private Organization's disbanding and our fleeing from United Nations Forces, we suddenly found ourselves coming under attack from unknown persons who utilized Powered Armour Units and called themselves the Transnational Security Office." The former pilot continued. "For the next ten years they destroyed every facility they could find that maintained a relationship to NERV in some form. They killed any personnel who were loyal to Commander Ikari and SEELE without question, regardless if they surrendered or not. Their bodies were crucified above the ruins where the battle occurred as a threat to any who were allied with Commander Ikari, SEELE, or anyone like them in the future'."
"And what evidence do you have to support these claims?" Misato asked.
"Commander Ikari has his plan written and documented in extensive detail. The part that involves Pilot Ikari is in a particular file known as Operation: Yesod." Rei Q explained. "As the commanding officer of the unit responsible for the direct implementation of the Human Instrumentality Project, I was mentally programmed with all the information relating to Commander Ikari's plans and how they are to be carried out."
"But why are you telling us all this?" The Colonel asked.
"I'm no longer under the control of Commander Ikari anymore. I have felt something reaching out to me. It feels very familiar for some reason, like that of a family connection. So I wish to why I'm being reached out to."
"Thank you, Dr. Akagi and myself will return shortly." Misato told the clone.
With that Misato turned to Ritsuko and gently nodded towards her. With that both women got up and left the room, with the cell door sliding behind them.
"If what she said was indeed true, then it would mean we've been fooled all this time. We would've played right in to Commander Ikari's plans." Ritsuko remarked.
"But then again, what if she is still under his control whether she knows it or not?" Misato stated. "We can't take the risk."
"About that." Ritsuko replied. "I carefully looked over her mental, nervous, and circulatory vitals while you interrogated her, and I what I saw was that there was no jump or change in her vitals. Moreover from what I saw, she her mental waves were equivalent to those who expressed a deep sadness. I think..."
Eventually Ritsuko was cut off by the arrival of Lt. Maya Ibuki.
"Sorry to interrupt, but Colonel Katsuragi, Lieutenant Colonel Akagi, the dissecting of Synthetic Mechanized Combat Aircraft Unit-01 is complete and we've extracted the Vehicle Data Recorder as you've ordered." Lt. Ibuki announced. "However there's something I think you should see from the recording."
"And why is that Lieutenant Ibuki?" The Colonel questioned, losing her patience.
"We found that the records recovered from Unit-1's data recorder don't match the investigation report that was provided to the United Nations by NERV before it's disbanding or the report released by the International Evangelion Project Agency." Lt. Ibuki replied.
"Have the records forwarded to my ready room, I'll view them there."
"Yes ma'am."
Epic of Evangelion
Misato and Ritsuko were in the Captain's ready room aboard the IAV Miracle. It was located just below the bridge of the ship and it had pretty much the same design as every other room on-board. White panels from roof to floor made up the walls, with a metallic floor, while a white light (dimmed this time) shone over them. A desk in the same make as the walls, built in to the floor stood in the middle of the office. Built in to the desk itself was a number of laptops and monitors along with a red and white phone for essential contact.
Both Misato and Ritsuko sat behind the desk watching the recordings on three separate monitors. The monitor on the furthest right showed Shinji's cardiovascular rates and mental waves, the furthest left monitor showed the outside with Unit-01. The screen showed Unit-01 hovering in the night sky above Tokyo-3.
The mech itself had a bright crimson red that replaced it's normal neon green accents. Clouds begun to swirl around it as lighting from the clouds begun hitting it multiple times at once. By this point they were 1.5 minutes in to the recording. Eventually Ritsuko switched the forward view on the left monitor to further out. Suddenly a shockwave originated from Unit-01 as it decimated all of Tokyo-3 and the surrounding area. After that, debris of broken skyscrapers, roads, and chunks of land slowly started to circle around the origin point of the shock wave. Then the vortex swirling above Unit-01 begun to steadily expand outward as high-speed winds begun to rip the surrounding area apart.
On the middle monitor, the cockpit was engulfed in a bright oceanic blue. Shinji was crawling out of his seat as he was reaching his right arm in to what seemed to be a pool of water. Suddenly, he pulled out a naked girl with white glowing skin. It was soon made out by Ritsuko and Misato that the girl in question was Rei. As Rei was pulled out, Shinji pulled the girl in to his embrace. What followed was probably the most emotional moment of the entire recording.
"Thank you Rei," Shinji thanked her. "...for trying to bring me and my dad together."
"I'm sorry I couldn't." Rei replied, sad and regretful of her failure. "I wanted you to be happy."
"It doesn't matter." Shinji stated as he closed in and hugged Rei even tighter. "This is all I need."
Suddenly, the blue stream of light surrounding Shinji and Rei quickly dissipated as the cockpit went back to it's normal colour. They suddenly saw Shinji letting out a short but loud shriek, before collapsing unconscious back in to the cockpit chair. Suddenly the recording cut out. Shinji's vitals at the same time went flat as well. Both women realizing that that was the end of the feed, decided to shut all off the recordings entirely until they saw that one of the monitors was still playing.
Except this time, it was not something they could remember during the day they witnessed Third Impact first hand. Unit-01's red glowing accents suddenly dissolved as its red eyes suddenly disappeared. The vehicle then begun to electrically spark all around as it started convulsing as if it were a person having seizures. The vortex of clouds circling above it suddenly disappeared as the mech started to fall towards the ground. At the same time, the debris circling around Unit-01 started to fall and smash the on the ground. All that was left was a clear night sky with a full moon above. By this point the ground looked nothing more then a wasteland charred in nuclear-powered firestorms. Much of the ground was now reduced to soot and ash as debris was haphazardly place everywhere, remains buildings standing lopsided, trees blown over.
Ritsuko was personally shocked at the revelation. But more at the fact that Shinji's vitals went flat near the end. It would mean he essentially died. But when he was retrieved by WILLE, his DNA was an exact match to the original, even his dental work.
"This isn't possible." Ritsuko thought to herself. "It's not scientifically possible for someone to come back to life. It could be that the Angelic Contamination revitalized his body and took control of it, but then we would know unless we're dealing with something completely different."
Ritsuko then turned to Misato to tell her about what she realized, only to see her commanding officer leaning forward in her chair, her bangs obscuring her eyes.
"All these years, we got him back, and I still treated him like the enemy... I wanted to blame him... I had to blame him... for everything these past 15 years. And deep down I knew something was wrong. We all got played... and it was because of me... all because I wanted revenge."
"Misato, nobody could've predicted this would happen." Ritsuko reassured her friend, putting her hand on Misato's shoulders. "All we can do now is move forward with our mission."
"But I should've known better Ritsuko. We all should've known better." Misato frantically shot back, before calming down. "I couldn't face losing everything again, and because of that... we were played by NERV for 15 years... and we didn't even know it until now. Now we have Shinji back... We can't go on like this Ritsuko, something needs to be done..."
Suddenly a beeping noise came from Misato's handheld transceiver in her coat pocket. She pulled it out only to find a secure line from Shinji's doctor on the IAV Miracle, Ft. Lt. Sakura Suzuhara show on the device's screen.
"What is it, First Lieutenant Suzuhara?" Misato asked, regaining her composure.
"It's Ikari, he's unconscious." the young medical officer panicked. "Severe bleeding from the nose and mouth. What's more his eyes are glowing red, almost like their flickering."
Misato and Ritsuko looked at each other shocked. The fact that Shinji's eyes were glowing red was evidence enough they had to intervene themselves.
"We're on our way." Misato replied over the transceiver as both women ran out of the room and towards Shinji's cell.
Epic of Evangelion
As both women arrived in Shinji's cell, they saw Sakura kneeling beside him, tightly holding on to his hand, begging him to stay with her. They then quickly turned their attention towards Shinji. What Sakura said was right, the boy's eyes were flickering a bright crimson red as streams of blood was pouring from his nostrils, forming a small puddle of blood below him.
"Suzuhara, what happened." Misato asked.
"I was coming by to take his vitals when I suddenly found him like this." The young girl explained. "When I arrived he was severely malnourished, his brain scans showed that his mental activity is extremely volatile, and his nervous system was causing him seizure."
"Very well. I'll take him to the Specialized Care Center on-board. Lieutenant Colonel Akagi, please wait for me on the bridge. First Lieutenant Suzuhara, I need you to accompany me and watch over Shinji." Misato ordered to both of them.
With that, Misato took Shinji in her arms as she carried him to the vessel's Specialized Care Center. Sakura soon followed behind, her arms filled with her unpacked medical equipment. Ritsuko stood at the side to let them pass before she made her way to the bridge.