A/N: Sorry about the cliffhanger on the last chapter. I thought I'd channel my inner J.J. Abrams for a change.

CHAPTER 40: THE OLD AND THE NEW

There was no logical explanation for it: Rei had a bullet lodged in her hip. The surgeons were able to remove it without difficulty but that still left unanswered questions. Ballistic examination determined that it was a 5.7mm round fired from Sergei Tokarev's handgun. But again, that left more questions than answers: the only time he fired that pistol since arriving in Japan was in his fight with Shinji; and Rei was, by that time, absorbed by the angel. Her gunshot wound was also located in the same location Shinji was shot, and, judging by the powder burns and the torn flesh around the entry wound, it could only have been made at point-blank range.

When Rei awoke after her surgery she had no answers either. She had no solid recollection of her time within the angel or Unit-01, only bits and pieces. She did recall a school, but not the one she and the other pilots attended, there was also a car accident, an entry plug and an image of Shinji in a wheelchair. She also had no idea how she had gotten shot nor how she got out of Unit-01. Her only explanation was what she told Misato, "Shinji saved me."

Oddly enough, the hollow point had concaved onto itself instead of flowering. Following her hunch Ritsuko had the bullet cut open and the tissue extracted from the outside of the bullet was a clear match with Rei's. But, the DNA sample taken from within the collapsed hollow point belonged to Shinji. It was a verified scientific 'What-The-Fuck' moment for Doctor Ritsuko Akagi, M.D., PhD. She had plenty of theories, but with no way to test them, she had no answer for Commander Ikari.

"I apologize, Commander," she said the day after Rei's surgery. "But there is no data-supported explanation for what happened. The First Child's recovery and subsequent injury defy logic."

"You do not believe that this was a result of the recovery operation?" The Vice-Commander queried. "Or a side-effect of the procedure?"

"I considered that," Ritsuko nodded. "But if it was then both pilots should've been expunged. I also considered the possibility of it being the end result of Unit-00's remains being absorbed by Unit-01 but…with no data to back that up…"

"I see," Ikari spoke up. "What about Unit-01's viability?"

"A test with the Dummy System was conducted this morning," Ritsuko replied. "The result was negative. The Dummy Plug didn't even register with the EVA."
"I don't understand," Fuyutsuki asked, his eyebrows contorted in confusion.

"The EVA didn't even note the mere presence of the Dummy Plug. We inserted a regular entry plug and got the same result. For all intents and purposes Unit-01 is dead. We could try replacing all the internal systems but…"

"But?"

"The error wasn't coming from the computer system. I'd venture that it's the result of the S2 Engine now present within the EVA. It's possible that it's 'registered' to only one imprint…"
"The Third Child," the Commander deduced. "And without him…"
"Unit-01 is just a glorified statue."

"Thank you, Dr. Akagi," Gendo replied. "Continue looking into possible avenues to reactivate Unit-01."

"Yes sir."

"On a related note, what's the status of the other EVAs?"

"Unit-02 is operational," Ritsuko replied as she changed the screen on her data pad. "Only minor and mostly cosmetic repairs remain but it is capable of combat operations. Unit-04 is still 100% ready."

"Good," Gendo nodded. "Reassign the Second Child to Unit-02 and, as soon as Rei has recovered from surgery…"

"She should be recovered enough in a week and a half," Ritsuko explained. "I've already scheduled a synchronization test with Unit-04 for then. I've also ordered a new plug suit compatible with Unit-04's control system."

XXXXX

Nearly two weeks later Rei was discharged from the NERV infirmary. On her way out she stopped at the windows to observe the repair work being conducted on the Geo-Front. 'Shinji sent me back in his stead,' Rei said to herself. 'Shinji, I promise I won't let your sacrifice be in vain.' "I will fight…for you, Shinji."

"How are you feeling, Rei?" A voice approached from the side. She turned to see Misato Katsuragi walk up to her.

"I would ask you the same, ma'am," Rei replied noting the shadows under the older woman's eyes. She also took note that Misato was looking a little pale.

"I haven't been sleeping well since…" She paused. "I…I just came by to pick you up."

"I am ready to leave," Rei nodded. "If I may ask first, what happened to Shinji's necklace?"

"Oh," she reached into her pocket and pulled it out. "I guess…I guess he'd want you to have this." She then handed the trinket over to the blue haired girl. Rei gently took it from her and draped it around her neck. "I should also inform you that you've got a synchronization test with Unit-04 tomorrow."

"I expected as much," Rei replied. "I understand it uses a new control system?"

"Yes," Misato said as she led the girl to the elevator.

The next day was the Unit-04 activation test. Rei was wearing her new plug suit, black with dark purple accents. The armpits and shoulders were a dark red as was the collar. The wrist controls had been moved to the top of the forearms. The suit also came with a variant of the A-10 neural connectors that had a small mechanical arm that mounted a monocle in similar fashion to the IHADSS used in the Apache helicopter with the lens resting directly in front of the right eye.

The new system placed the HUD directly in the pilot's line of sight no matter what direction they were looking. Unit-04 was the first, and so far only, Evangelion to use the new system. Unit-02's interface system wasn't compatible with the system, though. For some reason, seeing Rei in the new suit reminded Misato of Shinji. She looked so 'tactical', dressed in black and that high tech eyepiece feeding data to her eye.

"Approaching critical mark. 3.8 more…2.7…2.2…1.8…" Maya read off the countdown as the activation test proceeded. In the chamber before them was Unit-04. It was identical to Unit-03 in every detail save the new control system and color scheme. While Unit-03 was mostly dark blue, Unit-04 had the same color scheme as Rei's old plug suit, with black arms, white torso and legs, maroon hands and boots and a violet neck. "0.3…0.2…0.1 and rising." The computer beeped as the borderline was cleared. Unit-04, the latest Evangelion had been activated. "Borderline cleared. Unit-04 has been activated."

"How are things with Unit-04, Rei?" Ritsuko asked the First Child who sat patiently in the entry plug. What differentiated this plug from the others was that Unit-04's central console was smaller, the cushions padded with memory foam instead of leather upholstery, and the more angular feel to the 'throne' that gave it an almost 'stealthy' look.

"It feels…empty," Rei replied as she shifted in the chair. "Unlike Unit-00 or Unit-01. Odd."

"Probably because of the construction method being different from the other EVAs. Let's start calibrating the HUD…"

Asuka walked into the control room looking for Misato. The Ops Director was observing the test as usual. What was unusual was that the test was now calibrating the new control system. Asuka was jealous that 'Wonder Girl' got to play with a new toy and not her. Because of its construction method, Unit-02 wasn't compatible with the new system. Though it could be retrofitted it would take over a year to complete the process and require literally gutting the EVA.

"So how's Wonder Girl liking her new toy?" Asuka asked in her patent-pending 'bitch' voice.

"Everything checks out green," Maya reported. "Optical sensors and data pathways are within tolerances. Everything the EVA detects is projected onto the small screen right in front of Rei's eye."

"Whoopie," Asuka sneered. "Of course it won't make her a better pilot."

"Not now, Asuka," Misato growled. She hadn't been in a very good mood for the past two weeks and did not want to have to put up with Asuka's shit.

"Nor will it keep her EVA from getting eaten again."

"Asuka!" Misato snapped at her. "Shut the fuck up!" The red-head recoiled at Misato's bark.

"Did you say something, Colonel?" Rei asked over the intercom.

"No, Rei," Ritsuko answered for her. "The Second Child is here and the two are just having a little drama. Nothing to worry about."

"I could hear both of them over the radio," Rei replied. "Too bad it doesn't have a 'mute' button." That's when everyone stopped what they were doing and just glanced at each other. A couple of the background techs pinched themselves.

"Was that…?" Asuka muttered.

"Sarcasm?" Maya finished the thought. "From Rei?"

"Rei," Misato got on the radio. "Did you just…make a sarcastic remark?"

"I…I'm not sure," Rei's monotone voice came back. "I just…said what I was thinking. Did I speak out of place?"

"No, Rei, it's fine," Misato said, sounding a little chipper. "We're all finished here. You can exit now."

"Aye, aye, Colonel," Rei replied before logging off.

'Now that's odd,' Misato said to herself as she marshalled Asuka out of the room. 'Since when does Rei say 'aye, aye'?'

XXXXX

The next day Asuka found the school almost completely deserted. Only herself, Hikari, Kensuke and two other students were present for their class. "I guess people are still fleeing the city," Asuka said to Hikari as they waited for the instructor.

"Can't say I blame them," Kensuke said from his desk. Seeing as how there was nobody else to talk to he figured he might as well engage the Red Death. "Toji's family left when he was transferred to New Osaka. And my dad insists my mom and I leave for her hometown outside Sapporo by the end of the week."

"My family is considering leaving, too," Hikari said meekly. "Every day, fewer and fewer students show up for class. I wouldn't be surprised if the school decides to close down due to low attendance."

"Man," Kensuke grumbled. "Never thought I'd feel upset at hearing that." He then felt brave enough to ask Asuka something. "How's Shinji?"

"Shinji…?" Asuka was about to say something, or snap at the otaku. But the truth is she didn't know what to really say since Shinji's 'status' was listed as 'UNKNOWN'. Not 'Missing' or 'Killed-In-Action'. But, 'Unknown'. "Shinji's…he's dead."

"What!?" Hikari shrieked.

"Th-that can't be!" Kensuke shouted. "I-I thought that he…? What happened?"

"I don't know!" Asuka bellowed. "His fucking EVA went berserk and he dissolved into Ikari-Soup!"

"Shinji's dead?" Hikari sounded really broken up. "He-he fought the Angels longer than anyone and so well that…" She buried her face into her hands. "I can't believe he's gone!"

"I know. I didn't think anything could kill him either," Kensuke said leaning his head onto his desk. "What about Ayanami? Is she alright?"
"As alright as she ever was!" Again with the shouting.

"Sorry I asked," Kensuke said as the school headmaster opened the door.

"You kids all go home," he said to them. "The city is quickly becoming a ghost town, especially for anyone under the age of twenty. Not even half of my faculty has come in for the past week. We'll inform your families when school starts back up again. If ever." And with that the students collected their things and left.

As he walked past, Asuka grabbed Kensuke by the arm. "Did you know Shinji fought in a war before he came to Tokyo-3?"

"It took you this long to learn that, Asuka?" The spectacled boy shot back. "That's been common knowledge here almost since day one."

"Don't get smart with me! Just-!"

"Alright! Alright!" He waved his hands to calm the Teutonic Tornado down. "Geez. Yeah, he fought with a Wolverine Resistance Group, or WRG, in Philadelphia. I actually found a picture of him alongside an American National Guardsman," he pulled out his iPad and showed her the photo of Shinji and said soldier giving a thumbs up to the camera.

"Holy shit," Asuka said as she recognized her former-roommate and fellow-pilot holding a Kalashnikov rifle. "I can't believe this."

"Believe it or not, Shinji's a combat veteran," Kensuke said as he left the school.

Her mind still struggling to deal with her latest failure, Asuka was now on the verge of a nervous breakdown. Everything she had thought about Shinji, his presence at NERV, even her ability to pilot an Evangelion was now in question. Looking back it all made sense though: his scars, his rough demeanor, his incredible combat skills…it was all right there in her face. Add to that the fact that everyone at school knew this but her, and that everything about it was obvious, and she still missed it. "What the hell good am I if I can't see the obvious when it's staring me in the face like that!?"

XXXXX

Back at the apartment things weren't any more chipper. Whenever she got home from work, all Misato would do is sulk. Even though Asuka was still around, somewhat, the apartment felt empty without Shinji. Although she had lived for the longest time alone, save for her pet PenPen, Misato had gotten too used to having Shinji around. Misato went to her fridge to grab another beer when the doorbell rang.

When she came back into the apartment she grabbed two beers, one for her and one for Kaji who didn't bother opening his. Misato opened hers but didn't drink from it. Instead, she left it on the counter and just went into the living room and lay down, too depressed to even put in an effort to get drunk. "I can't imagine how you must feel, Misato," Kaji said as he sat down behind her, his hand gently resting on her shoulder.

"Shinji was the first real family I had since…" NERV's Operation's Director wept.

"I understand," he began gently massaging her neck. "He'd become something like a little brother or even a son to me as well. I owed him a lot…" He brushed some hair out of her face. "You know, he saved my life once upon a time."

"When?"

"When he was still in America," Kaji explained. "You have no idea how impressed I was with him. If I had to march through Hell and fight through all its legions with only one person at my side, it'd be Shinji."

"He was that badass, huh?" Misato muttered. "I was beginning to think Shinji was invincible…immortal."

"Very easy to come to that conclusion, I agree." Kaji said as he reclined slightly. Misato instinctively scooted back into him, cuddling closer. "But I think you're making a mistake by looking at this like Shinji had failed." At that, Misato rolled over and glared at Kaji. But before she could retort the unshaven man continued. "Rei said it herself, that Shinji had saved her…" He looked back down at the woman in his arms. "I don't know what all happened inside Unit-01, but I like to think that, if only one of them could be saved, Shinji chose Rei."

"You…you think he chose to remain in the EVA and send Rei back instead?" 'That does sound like something Shinji would do,' Misato said to herself, looking at the situation in a new light. "But, how does that explain the bullet?"

"You got me," Kaji shrugged. "But, Ritsuko doesn't have any answers because she's not used to going with her gut feeling." Misato rolled fully over, draping one arm around Kaji.

"What does your gut say?"

"That Shinji did what he had to do, what he felt was the right thing to do," Kaji ran his thumb along Misato's cheek, wiping away some tears. "He saved Rei." And with that, Misato buried her head in Kaji's chest and fell asleep.

XXXXX

"This has gone on long enough," SEELE 03 exclaimed to the assembled group. The full SEELE council was in session now, with only the 'SOUND ONLY' monoliths as place holders. "None of this was in alignment with our scenario."

"This isn't the first time Ikari has gone outside the parameters of the proscribed scenario," SEELE 07 countered.

"But this latest incident with Unit-01 absorbing an S2 organ, a 400% synch ratio with its pilot, and a near Critical Failure Incident…we should've had a bell around Ikari's neck."

"The bell was there," SEELE 02 responded, "it just didn't ring."

"A bell that does not ring is useless," 03 argued. "We need to make sure it rings next time."

"Perhaps it's time we stopped trying to gain Ikari's cooperation," SEELE 08 offered. "Perhaps it's time to take matters into our own hands? Directly."

"That risks exposure," SEELE 01, aka Lorenz Keel, disagreed. "And exposure could still ruin everything at this point. There are still three Angels left, two of which must be contended with."

"I agree," 02 spoke with confidence. "We tighten the leash on Ikari and keep closer tabs on certain NERV personnel: the Commanders, Colonel Katsuragi, Dr. Akagi and the command staff."

"What do we do about our agent?" SEELE 04 asked next. "His performance has been less than fruitful."

"We've been careful about how we use him," SEELE 05 responded. "We know he's been in communication with someone in the United States. We've assumed that this is one of his associates, aiding him in the job we assigned him."

"However?" SEELE 01 inquired.

"Our sources within the US government have led us to believe that he may be playing all sides. To what end and for whom we do not yet know."

"He's a liability," SEELE 03 barked. "As soon as he's reached the end of his usefulness he should be eliminated."

"I agree, but how to do it?" SEELE 02 asked.

"Perhaps we can ruffle Ikari's feathers for a change by taking advantage of known grudges? There are a few within NERV who would welcome the opportunity to settle a few scores."

"Very well," SEELE 01 affirmed. "Begin making arrangements to have it dealt with. But keep a tight hold on it, we cannot afford to allow anything to get out of hand. Enough has gone wrong already and we must be careful to avoid causing any more."