A/N: Thanks for the reviews everyone. Also, it's not often mentioned, but remember everyone who was 20 and younger is now a year older. Shinji, Asuka, Rei ect. are 15 turning 16 sometime in the nearer future, but people like Maya and older are still 24 and older.

Oh, standard boilerplate. Everything's different because Shinji's different and Yui's advice.

Yay, people like Omake (humorous outtakes and plot bunnies, not different endings to those who may have been confused) Submit some and I'll refine it a bit, from any chapter if you want, the earlier ones need some.

Italics: Thoughts/Yui

#Text#: #Shinji's Lovely Suite#, ect.

Bold: Sounds

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#Nerv Headquarters: Experiment Station-02#

"2 ummm, how many is it now? I'll make it 28 days previous" (A/n: yay for author powers! Making stuff up is considered an art)

-----------flashback-----------

The orange Unit 00 is hooked up to the diagnostic cables and Rei is calmly sitting in the pilot's seat, the same void expression on her face as always. Shigeru and Maya are at the controls starting up the program for the activation test. Gendo, Fuyutsuki, and Ritsuko were standing in the control room as well, their eyes looking at the various screens and out the reinforced observation window.

Gendo looks at Unit 00, "Activate."

Ritsuko walks over to the Aoba-less bridge bunnies and begins, "Connect the main power supply and all circuits together."

Maya hit a few keys, "The main power supply connected. Starting the activation system... Voltage increasing to the critical point: 0.5, 0.2, rising!" So far everything was successful.

"Start the second phase of the activation system," Ritsuko stated.

"The pilot has commenced the joining," Shigeru checking the display monitor to his right.

"Start System Phase II," Ritsuko was pleased so far, what could go wrong?

On a large overhead display we see the thousands of circuits and an absolute neural borderline chart. The circuit count begins to rise.

"Synapses inserted. Junction started," Shigeru.

"Pulses transmitted," Maya initiated.

The chart of circuits had completely filled out. "All circuits are operational," Shigeru.

Ritsuko walked back to the Vice-commander and commander, looking out the window.

"The initial contact has no problems." Maya.

"Power has been transmitted up to the brachial muscle in both arms. There are no problems with the nerve links." Shigeru monitored the nerves.

"Checked. Up to 2550 on the list satisfied," Maya.

"Arrange for the third connection," Ritsuko stared ahead.

"Up to 2580 satisfied. Until the absolute borderline, 0.9, 0.7,

0.5, 0.4, 0.3, pulses are beginning to flow back!" 'Crap!' Maya started frantically typing.

"Problems encountered on the third stage. Rejection is setting in on the nerve center elements." Crap!' Shigeru joined her in the digital workout.

"Stop the contacts. Break the circuits up to 6th." Ritsuko said, voice growing louder. 'Crap!'

"Negative. The signal is not being received!" Maya "Unit Zero is out of control!"

"Stop the experiment. Shut off the power supply." Gendo 'This was unexpected...'

"Yes, sir," Ritsuko jumped in the chair and was the late start in the digital race, "Unit Zero's power supply has been switched to standby."

"35 seconds until complete standstill," Shigeru's thought's 'Holy #$#$ I wish I were Hyuuga now!'

"It's dangerous--step back!" Ritsuko shouted as the beserker slammed against the window where Gendo was in front of her, 'Is it after me?' Dumb fake blonde moment as the glass bent in towards to the stoic Gendo.

'Such a temper, we will try again next week.' Gendo was confident of the inability of the Eva to mess up his scenario.

'Uh oh' Maya stated in disbelief, "Auto ejection system engaging..."

The commander eloquently realized, "Damn it!"

"Time until the complete standstill: 10, 8, 7... " Maya 'Poor Rei...' The entry plug slammed against the ground.

"Special Bakelite. Hurry up!" 'I do not look forward to next time with Gendo,'

"Rei!" Oh my God! He has a heart...a sick bastardly heart...

"6, 5, 4, 3, 2, 1, 0." Maya finished.

Gendo was out of the room and on his way to the experiment bay. Little weak man legs pumping as fast as possible. He finally made it to the superheated hatch and placed his hands on the manual hatch. Psssssh! If only he had used his face to open it...

"Rei, are you all right? Rei!" Rei opened her eyes and stared at him, suppressing her pain.

"OK," Gendo stated, his scenario was not ruined, the dummy plug system was being rebooted and should have finished now... a sick bastardly heart that needed to be crushed into pulp.

---------------------end flashback------------------

Shinji, Ritsuko, and Misato were at the angel site following Ritsuko's lead. She was just about to answer a question Shinji asked as they approached a lab room. The question was "Have you seen Rei?"

"Ayanami Rei, 14 years old. 'First Children,' the first testee found by Marduk Report. The exclusive pilot of Evangelion Prototype Unit Zero. Her personal history was started afresh. All her records have been erased," she stated with eyes glassed over.

'I didn't ask who she was, jeeze!' "Not who? Where?"

"Well why did the activation mess up last time?" Misato inquired. 'Hasn't she been doing it for months?'

"We still don't know for sure. We think it was mental instability in Rei."

"Mental instability? In REI?" 'And PenPen is God...'

"Yes. She was much more disturbed than we expected." 'Unless...'

"You know, this is real interesting debating Rei's level of insanity, but where is she!"

"Oh, hi Shinji. She's at NERV for special testing before the re-activation." 'Inside of a giant tube nonetheless so we're prepared to make a new Rei.'

'Oh, she's inside the giant tube in the Reiquarium, why didn't she just say so?' Don't worry he's not stupid, just sarcastic.

An announcement was heard: "Demolition of Block-D3 has finished. Please submit all data to the Analysis Group of the 1st Division of Engineering Bureau." An open passageway to the left revealed the core of the fourth angel, bullet hole as big as a small car.

"So that's the enemy," Shinji was happy with the last battle results. The other stooges weren't, they had their asses handed to them as much as possible. There weren't any laws per se that they violated but they got chewed out by a lot of people. "Why the hell do we call them angels? And what happened to the first two?" Shinji stood in front of Ritsuko with a curious expression.

"Erm...That's the name that was agreed upon by NERV, Marduk, and other world organizations. The other information is classified." 'Shinji-kun has quite the mind.'

'Wait...what did happen to the second? I know the first blew up and caused Second Impact,' Misato wondered.

"OK Ritsuko, at least they're dead. I mean only someone completely messed up would keep them alive."

"Right. Well, thank you again for the sample. All the parts are intact except the core," she answered truthfully.

"Do you know anything new?" Misato decided to ask her other question later.

Ritsuko walked to the computer and pointed to the inanalyzable screen. "Nope, not really. We just confirmed some old hypothesis though. We know the Angel is composed of matter which has the properties of both particles and waves, just like light."

"Wait," Shinji spoke up, "that's BS! All matter as a wave-particle duality nature. You might as well be saying it's organic styrofoam."

"Ignore the plothole Shinji-kun, did you find anything out about it's power system?" Misato was interested in knowing if a self-powered Angel killer could be made.

sigh "No..." Ritsuko wasn't feeling well about the recent developments, time to show them something that would make her feel smart again. "Look at the inherent wave pattern..."

Misato looked as well as Shinji, both had no clue what it meant, even with Shinji's future knowledge. Then Ritsuko hit a key to compare it to a human's DNA.

"Pretty graphics..." Ritsuko and Misato stared at him. "Erm, what? They're very similar."

"That's what I'm getting out of it too," Misato spoke.

"Right. Although the constituent elements are different from humanity's, the arrangement and coordinates of the signals are extremely like humanity's genes: 99.89 comparison," Ritsuko felt better now.

"That means..." Misato began.

"Yep, it looks like we know barely anything," Shinji was comparing and uncomparing the strands of data to observe the pretty graphics. Ritsuko had wanted to say that.

"OK. All right. Stop it," The engineering supervisor was talking to a worker across the hall from Shinji's group. Gendo and Fuyutsuki had arrived and were looking at the angel.

"This is the core... How is the rest?" the vice commander addressed the supervisor.

"The degradation is very serious. It isn't suitable for a sample."

Gendo butted in, "No problem. Discard all other parts."

Misato looked at Shinji, "Hey, something the matter?"

'Besides the fact I can't shove the bastard over the railing to his death?' "I do not like being near him, he doesn't care about anyone but himself unless it furthers his $#$#ing scenarios. Can I borrow you gun Misato? Just turn the other way and give me a minute."

"Haha Shinji," 'Definitely issues there' "Hey Ritsuko, do you want to come over for dinner? You have to try Shinji's cooking!"

"I love how you didn't ask me, but sure. What do you want to eat Ritsuko?" Shinji didn't really care much anymore.

"Sorry, but I can't today. Is tomorrow alright?"

"Sure." "Fine with me."

-----------------------Outside at PE the next day--------------------

The girls were swimming or sitting against the fence and most of the non-spectator guys were playing basketball. The stooges were sitting on the hill for their rotation out of the game.

Toji was bluntly staring at the girls, if you listened you can hear one girl say, "Suzuhara has a weird look in his eyes!" (A/N: Really, it's in the series)

"All the girls have great bodies," Toji stared on despite hearing the comment before noticing Shinji was looking as well. 'Why don't they ever say anything about him looking?' as a few girls waved and Shinji waved back before turning back to the game.

"Hey, who were you checking out?" Kensuke piped in.

"No one in particular..."

"My guess is Ayanami," Toji retorted.

Before Kensuke jumped in, Shinji's bastard side acted up before he could suppress it, "Hikari is just as good, she's the most developed for are age with Rei not far behind," 'Unitl Asuka comes.' "Do you think she'd like a bento from me Toji?"

"No! err...I don't think so." Toji was pissed and embarrassed at Shinji.

"Oh, so that's who you keep staring at...what do you like? Horaki's breasts, Horaki's lips, and Horaki's..."

"thighs!" Shinji and Kensuke finished. Toji was denying it vehemently. Kensuke liked the turn of tables after Shinji arrived, less of him being an Otaku and more of the other two arguing while he sells admission.

"Sorry Toji, couldn't help myself. I know you don't like her," Shinji tried to appease the jock. "I was really watching Rei, she's always alone and I can't seem to get a conversation out of her."

"Yea, she hasn't made any friends, well maybe that tree outside the window..., since first grade when she arrived," Toji calmed down, he didn't know that Hikari was paying slightly less attention to him lately. It didn't occur to him that she was originally attracted to his outgoing personality and body... and now there were two available on the market.

"She just looks unfriendly, I don't know why," Kensuke mentioned while thinking, 'Blood red eyes, blue hair, and white skin...she must be an alien escaped from a military facility.'

"I think I'll start making her some bentos, maybe she'll warm up to everyone once she has a friend."

"Why are you so concerned? You like her right?" either stooge, take your pick.

"I guess, I don't really know honestly, maybe I'll just ask Hikari out for simplicity," Shinji said as he jumped up and they rotated into the game, enjoying the fuming Toji and laughing Kensuke.

-----------------------Dinner at Misato's with Ritsuko------------------------

Shinji was serving the meal as PenPen, Misato, and Ritsuko stared at him. He finished by placing some shark fin soup he made for PenPen and sake in the water-fowl's dishes.

'How PenPen has a high enough tolerance just to get a buzz from that amount amazes me that he hasn't died.'

Finally Shinji sat down at the table, Ristuko had not had Italian in a while, but still knew this was going to be the good stuff. He slid Misato her Yebisu and said, "Itadakimasu. Eat up."

PenPen dived into his dish and the other parties present ignored the slurps of pleasure. "This is great, I haven't had this in years!" Ritsuko was shivering with delight as she was sorely attempted to follow PenPen's example...Misato wasn't.

"See, he's the cooking god!" Misato spoke up from her plate and held her hand in the air as another Yebisu flew into it courtesy of Shinji.

"Shinji-kun, you'd better move out. You'd better not let your ill-behaved roommate ruin your life." this was ruined as her own belch that rattled the silverware. "Excuse-me..." Ritsuko was red and Shinji/Misato were laughing there asses off.

"That's okay, at least I know you like my food. Maybe you'd like to have me be your roommate?"

"Sure." "NOOOOOOOOO!" "WAAAAAAAAAAARK! (I'LL KILL YOU!)"

Misato was frantic, PenPen was going for his sword collection to start the cat hunt, Shinji and Ritsuko were smiling evily. Ritsuko sadly realized something.

"Damn! I can't! He'd have to cut through an incredible amount of red tape. Shinji-kun just received his formal security card, you know," as she handed the card to him. 'Damn, we could have had so much fun...Bad Ritsuko! What the hell? Where did that come from!'

Shinji noticed the range of emotions on Ritsuko's face, of course he had to ignore the clank of PenPen dropping a katana and beginning to celebrate with Misato, "Is there anything else I can do for you Ritsuko?"

"There is actually, Ayanami Rei's renewal card--I never got the chance to give it to her. I'm sorry, but would you please deliver it to her home on your way to Headquarters?" She handed the card over before getting the response, doesn't it feel great when that happens?

Shinji looked at the card for a moment and set it on the counter as Misato began to say something.

"You were staring at the picture, eh Shinji?" Misato started to tease him.

"What was that Misato? You're cleaning up the dishes or I'll sic PenPen on you?" Shinji placed his hands in front of his face, assuming bastard-no-glasses form.

"Uhhhh"

'That's scary,' Ritsuko's thoughts, "Stop that, I'll help Misato even."

"Thank you," Shinji returned to normal, "is there anything in Rei's past that has made her almost mute?"

This hit a little home with Misato as she filled the sink with water. Ritsuko next to her answered, "I'm not sure, I just believe she's not very good at living."

"I'm going to try to change that, it would be great if I got some help."

Misato answered immediately that she would help when it was possible and Ritsuko agreed. Misato added though, "you have my full permission to ask her out Shinji-kun, I can afford to let her have my cooking god for a night or two."

Shinji headed off to his computer to order some things, 'Rei won't know what happened, mom will be proud of me.' He sat down and counseled with PenPen for each of the purchases.

----------------------Outside Rei's complex the next day-------------------

In an alternate universe, one would know that Rei lived in a run down complex, which makes no sense since the city's new. I errr...we see Ayanami's building, it was one of the newer buildings as her old place was condemned after it collapsed. Her neighbors had moved away after the angel attacks, but the other floors were half-filled. A truck pulls away and Shinji waves good bye. It was earlier in the morning than last time and Ayanami's alarm was about to go off.

Beep Beep Beep click Rei turned off the alarm and rose from the bed. Avoiding the bandages that were on the hardwood floor she headed to the kitchenette to prepare her breakfast,

Ding Dong 'No one was scheduled to be here. Who is it?'

"Excuse me Ayanami, it's Ikari. May I open the door?" 'Why she doesn't lock it I never know.'

"Come in," Rei started preparing her meal.

"You heard her let's move it in!" Rei heard pilot Ikari say and paused.

Shinji met her in the kitchen and she looked back at the noise. She was only wearing a white shirt and white panties. "Hey, I made you breakfast. Let's eat it on the balcony," Shinji pointed to the table and chairs that were not there before. He handed her the breakfast bento and shooed her as best as possible to the balcony.

Rei was confused, she didn't show it well as she opened the boxed breakfast. It was an acceptable alternative to her schedule and saved her time so she started to eat with Shinji.

"I hope you like it, I don't get an opportunity to cook vegetarian often. I made sure it was acceptable with your nutritionist so dig in." Shinji had learned that meat posed an unacceptable chance of contamination to Gendo's plan to unite her with Lillith, who cares if it was only a .00000000000000001 percent chance, the bastard wanted all variables to a minimum. 'At least I know Rei isn't allergic to it...maybe I'll sneak her some for fun later.'

Rei was eating away, slightly faster than normal, but, 'This tastes...good. Pilot Ikari is a good cook.' She looked back to her apartment and then to Shinji as she finished off her water. "What is occurring in my residence Ikari-san?"

"I decided to surprise you with a gift, I came the other day, but apparently you were in special testing at NERV for preparation for re-activation. I saw your apartment wasn't furnished completely, so I decided to buy you some stuff. I hope you like it." Shinji watched as the moving supervisor opened the sliding door.

"We're all done Mr. Ikari, thank you for your business."

"No, thank you. Here's a tip for all your men," Shinji handed a large wad of cash to him and waved good bye. The men all smiled back and left, what a nice kid to furnish his apparent girlfriend's apartment and leave them a huge tip.

Shinji picked up the remains of the meal and placed them in the empty trashcan. Rei had followed him. "Why did you purchase these items Ikari-san?"

"I did it because I believe you deserved it for everything you've done and call me Shinji, not Ikari or Ikari-san or pilot Ikari. Now let's look around!" Shinji dragged the even more confused Rei into her room, he was glad he took caffeine pills that seemed to counteract the dreariness Rei broadcasted.

They walked on the soft rug to her closet and he showed her a few extra outfits she could wear to NERV or on days off. Then he showed the new dresser still had the commander's glasses and now a picture of himself, PenPen, and Misato smiling. The desk was no longer littered with bandages and her bed had large fluffy pillows and a comforter. There was a mirror and few pictures of nature hung on the walls, blending nicely with the new curtains.

Her room was nice, different than what she was used to, but nice. Every time she tried to say something, Shinji pointed out something else new and dragged her to a different part of the apartment, ending with a bathrobe in the bathroom. 'Why? I do not understand.'

"Thank you Ika..." Shinji stared at her motioned for her to sit next to him on the bed.

'This is very soft but,' "Thank you Shinji. However, I do not comprehend why? I should not accept this..." Rei looked at her new surroundings, she felt a little more full for some reason.

"You're my friend Rei, even if I'm not your's. This is a lot more than any gift between friends is normally. I just want you to enjoy life, have friends, and realize there's an infinite amount of possibilities of anything happening. There is no one set path, so I figure I'd start with your home so you can choose your life."

"..." 'I am Ikari's friend? He wants me to live the way I want. What do I want? Why is this happening?''

"Heh, you look confused Rei," 'That's new,' "don't worry about it, I'll be waiting outside when you're finished with your shower and dressed. Wear one of your new outfits, I have your new security card when you're finished." Shinji left the apartment and slumped against the wall, it was tough stating things as friendly commands and keeping up a happy attitude knowing a giant angel that was almost impossible to beat was coming that afternoon.

Rei, on the otherhand, tried to continue her usual routine but was constantly reminded of Ikari's generosity. New soap, new shampoo, little shower flowers on the floor, a fluffy robe, a new outfit. 'Which one should I wear?' She noticed a sticky-note on something that resembled her uniform, except a few color differences and a long sleeved light coat. #Wear this if you're confused Rei, Shinji#

Shinji finally stood up as Rei came out, she had chosen his outfit. Eh, it wasn't bad, nice and not too different. He handed her the updated security card, "You know Rei, you should've smiled in the picture. I bet you're cute when you smile." 'Come on...'

The edges of Rei's lips turned up for a split second, resulting in a small smirk before she placed the card in her pocket. 'I feel warmer, this coat must be wool' "..."

'So close, but what did I expect, oh well. She's better than last time,' "Let's go Rei, you have a activation test to ace!" Shinji left and Rei followed, Shinji popped another caffeine pill and slid his card through the gate, parting ways with Rei as he headed to the control box.

-----------------------------------That was a long scene to type------------------------------

Rei was in the entry plug, mind focused on the present task despite the constant questions of this morning popping up. Everyone else was in the control room and Shinji complained that there was no popcorn.

Gendo was in charge and more active this time, "We're commencing Unit Zero's reactivation experiment now. Start the first connection."

Ritsuko was sitting down at the control next to Maya who didn't mind at all. "Connect the main power supply."

Maya replied, "Voltage has exceeded the critical point."

Ritsuko volleyed back, "Roger. Move the format to Phase II."

Shigeru not to be ignored, "Connecting the pilot with Unit Zero."

Maya rebounded with, "Opening the circuits...The conditions of the pulses and harmonics are good."

Shigeru fired his last shot, "There are no problems with synchronization. All nerve links are completed. Nerve center devices are operational."

"Checked. Up to 2590 on the list satisfied. Until the absolute critical line, 2.5, 1.0, 0.5, 0.1, and rising! Borderline cleared," Maya knew she had the better lines, "Unit Zero has activated. Whoah! Sync ratio's at 50 and climbing steadily."

"..." Rei was silent, Shinji and Misato were not: "Keep it up Rei!" "Way to go!"

Fuyutsuki had to ruin it, "Ikari, an unidentified object is approaching. I think it's the fifth Angel."

"Thanks, I'll get dressed. You should tell the commander now," Shinji sprinted out of the room as Gendo stared at Kouzou. He nodded back to the commander.

'How dare Kouzou.' "Interrupt the test. All hands on first class alert."

'Please don't hurt me.' "I was talking to you, not the third child and why not use Unit Zero?"

Gendo retorted, "It's not yet ready enough for battle. How is Unit One?" He directed towards Ristuko. 'That does make more sense, why would he tell the third child before me?'

"It will take 380 seconds to prepare it." as she packed up to move to the main control room.

Gendo commanded, "Sortie! Rei, we've comleted the reactivation. Come back." Gendo took his personal elevator to the command deck, leaving Fuyutsuki to walk. Gendo sat back in the chair as he watched Unit 01 prep.

Smack! The back of his new chair fell off and his ass hit the floor. He had just got this damned chair this morning. He didn't notice the monitor of Shinji laughing at him.

'HAHAHAHAHA! That was great Shinji-kun,' the power had been connected and he was now syncing.

Shinji wiped a tear from his eye before responding to his mom, it was well worth the tip he gave the moving men. 'Yea, I'm worried about this angel, I didn't like being deep-fried in LCL before,'

'And I enjoyed a the massive case of heart burn and melting skin?'

"Shinji, are you ready?"

"Hell no Misato, let's do this!"

"Eva Unit 01 Launch!"

Shigeru was monitoring the angel, it was a nice blue octahedral with no obvious core or head. It was slowly floating to the outskirts of Tokyo-3. The evacuation sirens were blaring and people disappeared off the streets as the elevator carrying Unit 01 neared the surface.

'You know it's too bad I can't completely eliminate my AT field so it won't notice me...'

'Shit' Shigeru shouted, "High-energy reaction detected inside the target!"

"What!" Misato hoped she didn't hear that. It was never a good sign.

Shigeru continued, "Its circumferential parts are increasing speed and concentrating!"

Ritsuko realized it, "That means..."

Remiel fired a shot from the equatorial corner pointed at where Unit 01 would pop up. The elevator hit the surface, the evil pretty beam of death on target, headed straight for the cliffhanger!

---------------------------OMAKES LATER-------------------------

A/N: Yep, an early update to surprise you. And an evil cliffhanger to enrage you.

No real explanations I can think of, any errors are because I rushed to put this out, oh most comments I've made have been deleted since most chapters are older now.

--------------------OMAKE (only 2 boring ones, it's what you get for a quick update)----------------------

What happens when you don't have thumbs...

Shinji noticed the range of emotions on Ritsuko's face, of course he had to ignore the celebrations of Misato, "Is there anything else I can do Ritsuko?"

"There is actually..." Thwuck! Ritsuko's eye's widened and looked down to the fallen form of PenPen. She was currently held to the wall by three katanas that he had been carrying. They had pierced her clothing and her feet were dangling above the floor as she couldn't pull out the swords. "Excuse me, but could you?..."

"Sure...umm, your stuck." Shinji and later Misato couldn't budge the swords.

"PenPen apologize to Ritsuko here," Misato scolded and he waddled up and warked a few bars. He then came running back with a knife.

"Noooooo!" Ritsuko screamed. Shinji grabbed the knife and cut Ritsuko's clothes off so she could leave. She didn't know PenPen had stolen Shinji's camera and taken a picture. It was time for him to report back to Yui.

Misunderstanding (Warning, highly perverted and upper teen rating)

...a new outfit. 'Which one should I wear?' She noticed a sticky-note on something that resembled her uniform, except a few color differences and a long sleeved light coat. #Wear this if you're confused Rei, Shinji#

Shinji stood up as Rei came out. Shinji's jaw dropped and started to drool. Rei took some meanings too literally.

She was wearing only the sticky-note...well, she was a natural blue head for sure. "Do you have my security card Shinji?"

"Yea...where are you gonna put it?" She smirked for a second, took the card, and walked on to NERV empty handed, in a clear voice "Are you coming Shinji?" Shinji's mind couldn't take what happened and his nose exploded.

(If you don't know what happened, do not try to figure it out)

Review if you want