Okay, now everything in here isn't exactly the same as it is the the main storyline. The vast majority of it should be, especially in later chapters, but like i said, this is an alternate story that takes place instead of the movie. This takes place after episode 26, meaning 25 and 26 both happened in my story, so...Enjoy.

Disclaimer: I don't own Evangelion.

Episode 1: Instrumentality

Shinji Ikari was on his side on his bed. His eyes were fixed on the plain white wall of his room in Misato's apartment. The moon was the only source of light in the dark room. Headphones ran from Shinji's ears down to an object in his hand that had died a few hours ago.

"Asuka," Shinji whispered before rolling onto his back and staring at the ceiling of his room. "Kaoru,"

Case Number 00: Ayanami Rei

Rei sat on a small wooden chair. Her expressionless gaze was fixed directly ahead of her. She was wearing her school uniform and had both hands folded on her lap.

Who are you?

"I am Rei Ayanami," answered Rei.

Who are you?

"I am Rei Ayanami," Rei said more confidently.

Are you sure that you are you?

"I don't understand the question," she said.

Do you know who you are?

"I am the third, correct?" Rei responded. Images of Rei as a young child and then as a teenager in bandages flashed in front of her.

So you're nothing more then another copy?

"No," Rei answered. Her crimson eyes narrowed.

How are you sure?

"Because I decide what it is I do," Rei responded.

So this makes you an individual?

Rei looked down at the floor. She was confused. What was going on?

"First child," said a deep voice. Rei looked up to see Gendo Ikari staring at her with one finger on his glasses. "Do you know where you are?" Rei stared at him. "This is instrumentality,"

"Instrumentality?" Rei asked.

What makes you an individual?

"I'm not certain," Rei answered.

So you actually are nothing?

"No," Rei responded. "I am something,"

You are the third, nothing more,

"That isn't entirely correct," Ritsuko Akagi was standing on the stage where Rei sat. "Although the receptacles that are Rei all do the same job of housing a soul, each carry their own individuality." As Ritsuko spoke, the sight of the area where the other Rei's were kept in LCL appeared. "For example, the Second held an emotion that was so close to, that it might be construed as love towards Gendo." Rei speaking with Gendo and then Rei closing the case that held his glasses flashed in front of her. "However, the Third holds more a distant personality towards Gendo, or perhaps even dislike," The time when Rei broke Gendo's glasses played like a movie in front of her.

Why do you pilot the Eva?

"What reason do I have not to?" asked Rei. Shinji suddenly grabbed her by the shoulders.

"You could die in that thing!" He exclaimed.

"Then I guess I would die. That doesn't matter to me," Rei responded.

"But if you die this time, there's no way to come back," said Misato. "Ritsuko destroyed the others," Another scene played in front of Rei where the Rei's in LCL started to break up and die.

"Then I suppose I would cease to exist," Rei answered. "It doesn't matter to me,"

"Don't you think it matters to someone else?" Rei was in the entry plug after their battle with the fifth angel. It was the time that Shinji made her smile, but these weren't the words he had said then. "Did it even once cross your mind that someone would miss you if you were gone?" Shinji's tears hit Rei's cheek.

"Why are you crying?" asked Rei. This sounded familiar. Rei was back on the stage. A spotlight made her squint a little. "People would miss me," she said. "But what made him cry?"

You've cried yourself

"I have?" asked Rei. Rei was operating unit-00. It was the battle that she had activated the self-destruct sequence in the Eva. "Why did I do that?" Tears fell onto her hands. "Am I crying?"

Rei stood up from her seat. She was back on the stage in the spotlight. "This program is useless," she said calmly. "Please shutdown and let me go back to my home,"

Gendo watched as the Instrumentality project was performed on Rei. This program had already been launched on Shinji and everything worked out well. All Rei had to do was follow through with the program.

Everything was going well. The program was working as well on Rei as it had on Shinji. She actually seemed to be getting somewhere. Until she stood up and told the team to shut it down. That wasn't supposed to happen. As expected, Fuyutsuki leaned towards him to ask what should be done.

"Shut it down," Gendo instructed. If the subject refuses what is happening, then nothing can affect them, and he knew that once Rei's mind was set it would be difficult, if not impossible, to change it.

"Shut it down?" Maya said, turning in her chair. "But sir! That could damage the system!"

"There's no point in continuing with a hopeless subject," The screens in front of him returned to the plain white room that Rei had been sitting in. He pushed a button and began to speak into a small microphone. "You disappoint me, Rei. The third child did better," Knowing that Rei heard his words, he returned his hands to their trademark folded position. He spoke quietly, but he knew that Fuyutsuki would hear him.

"Get hold of Katsuragi," he instructed. "She shouldn't have any trouble getting Ritsuko to inspect the MAGI,"

Warm and inviting sunlight shone through Shinji's window. How deceiving. As if today would be that great. He hadn't had a good day in nearly two weeks. Not sense…

Shinji slowly pushed himself up and walked towards his door. He slid it open slowly and saw Misato with one foot on a chair to tie a boot. She looked up and smiled faintly, as if trying to seem pleased to see him.

"Morning, Shinji," she said. "Did I wake you? Sorry,"

"No, you didn't" Shinji said quietly. He decided he would continue the conversation. "Why are you up this early?" He knew Misato had the day off. Shinji was actually surprised that she even worked at all. All of the angels were dead. Even Kaoru.

"Well, Rei was at NERV last night," Misato said calmly. She'd finished tying her boot and was now adjusting her coat.

"The whole night?" asked Shinji with a little more enthusiasm then he would have preferred. Misato nodded.

"She was in the same project as you were," Misato responded before moving over to a mirror.

"…Instrumentality," he said, looking down. Misato answered with a confirming mumble.

"But something went wrong," Misato said. "Rei didn't take to it. They had to shut down, and now they need Ritsuko. They called me because she's still…well…" Shinji nodded, understanding. "Well, I'm off. If you're going back to school today, I've written a note explaining your absence the past three days,"

School had restarted in Tokyo-3 a little over a week after the announcement that the last angel had been destroyed (It was funny how that found a way to keep coming back and bite him in the ass). Only about half the students returned at first, Kensuke and Toji being among them. Over the last few days, a couple more families came back, but it would be a while before everyone returned to Tokyo-3.

Misato closed the front door and left Shinji alone. Shinji walked over to the counter and stared at the note. Misato's curly handwriting was almost as sloppy as her out of work.

Please excuse Shinji from School. There was a death in the family,

A hint of anger flashed across Shinji's face before he crumpled the note and threw it in the trash. Like he would go to school today. He closed the door to his room behind him. He couldn't face all of them. Not today.

"Awesome!" Kensuke exclaimed.

"Yeah, you would think so," Toji responded.

Toji sat at his desk lifting up his left pant leg. The prosthetic leg he now had sense the incident in the Eva felt weird. Sorry, it didn't feel at all. Maybe that was what was weird?

"Did it hurt, Toji?" Hikari Horaki, class president, bent down towards Toji to inspect the artificial leg. Toji dropped his pant leg and smiled.

"Nah," he responded. He looked up from his seat at the worried Hikari and smiled. "Nothin' really," Kensuke looked at Toji.

"But Toji, weren't you just complaining about how this would affect your basketball-," Kensuke was interrupted by a growling Toji.

"Shut-up!" he muttered to Kensuke. Hikari had broken out in a contained fit of laughter. She was clearly trying to hide it, and was just as obviously failing. Hikari choked down the laugh and started to wave.

"Well, I have to go," Hikari said. "See you later!" she jogged to what she was supposed to be doing. Kensuke was smiling menacingly. Toji just stared.

"Uh, what?" he asked. Kensuke smiled wider.

"You're going out with her, aren't you?" he asked. Toji's face burned red and he immediately stood up.

"No-no I'm not!" Toji stammered.

"Yes, you are!" Kensuke said louder. Toji shook his head furiously. The sound of the late bell echoing throughout the school made Kensuke look over to an empty desk. "Shinji's not here again?" Toji shook his head.

"Neither is Asuka or Rei," Toji said. Kensuke turned towards the window to look at the city.

"Do you think something happened at NERV?" he asked.

"You there! Stop talking or it's detention for all of you!"

The sound of the teachers voice made them all stand at attention. Still, Toji and Kensuke couldn't help but worry a little over what had happened to their friends.

Ritsuko Akagi sat in the darkness of the room she was in. The only sources of light came from the red glowing sign with NERV's logo and the recently opened door to where she was.

"Ritsuko,"

Misato's voice came as a surprise to her. She wasn't expecting Katsuragi to show up. But that meant Gendo had sent her for a certain reason, and Ritsuko thought she knew what she was going to ask of her.

"Let me guess," Ritsuko started. "He wants me to check on the MAGI?" Misato nodded. Ritsuko snorted. "Hypocritical bastard," she whispered.

It wasn't long before Ritsuko was crawling inside the base of one of the three computers. Technically, she could have run the check on the MAGI without having to go inside, but there was something she had to do.

Her lab coat was in a crumpled up ball next to her. Her fingers glided across the keyboard at an amazingly quick speed. She would have to link to the brain of the computer in a short while.

Ritsuko stopped typing and looked up at the protective plate on the computer. There were marks where she had opened the plate not to long ago to link to the computer. "I'm going to do it," Ritsuko whispered. "This is going to bring us closer," She slid her fingers over the plate. "Right, mother?"

A clean, white hospital room was silent except for the operation of medical machinery. A gentle beep came from the heart-rate monitor position to the left of the bed, opposite the door. It blocked most of the light from the window behind it, but what did get through illuminated the red hair and smooth skin of the patient.

Her chest rose and fell in the steady rhythm of breathing. A few wires ran from her wrists and chest to the machinery. Slowly the patient's eyes opened in the bright light. Asuka Langley Soryu woke up.

Asuka managed to make out the images going on around as the door to her room opened. It looked like that weird guy who assisted Ikari's dad was staring her in the eyes. It wasn't long before she fell asleep again.

Case Number 02: Langley Soryu Asuka

Asuka opened her eyes. She was sitting on a small wooden chair on what looked like the stage from her school. A spotlight illuminated her position. She stared up into the light, squinting.

Why do you pilot Eva?

"Because I can," she said. The answer seemed simple enough to her.

Why do you pilot Eva?

It just asked that question. Did it want a different answer? "I pilot it because no one else is as good as I am!" Asuka said, feeling some of her confidence return.

An image of Shinji flashed in front of her. Asuka's eyes widened. She stared directly at the image before slamming her eyes shut and putting her head in her hands. "No!" she screamed. "Don't talk about him!" The image of Shinji was still visible, even when she closed her eyes. "Get out of my head! I hate you!"

Do you hate him?

Asuka lifted her head. She was quiet for a while. "Yes," she said after a while.

Then why do you love him?

Asuka glared at the light. "I don't!" she defended. "Everything is his fault! I hate him!" A scene with her mother in the hospital flashed in front of her. Asuka's eyes narrowed and watered. "Mama," she whispered. Asuka shook her head. "She didn't do anything to me!"

Another scene played in front of Asuka. Her mother was holding a doll. "Come on Asuka," she said. "You have to eat all your vegetables. You wouldn't want that little girl over there to think bad things of you, would you?" She motioned towards a young Asuka leaning on a glass window.

Suddenly Asuka was staring her mother's tombstone as rain fell. A woman leaned over. "It's okay to cry, Asuka," A young Asuka was holding a doll and looked serious.

"I'm not going to cry!" she said. There was a flicker on the image and the young Asuka was suddenly crying. The Asuka sitting in the chair spoke.

"Why is she crying?" Asuka said. "I didn't cry then!" The young Asuka was in a grassy field. She was running. Asuka's eyes widened in horror as she listened to the familiar dialogue. The young Asuka spoke of how she was chosen to be an Eva pilot. How she was superior. Her smiling face contorted into a mix of confusion and sorrow as she opened a door. Her mother had hanged herself.

Why do you pilot the Eva?

Asuka felt a few tears slide down her cheeks. After a while she spoke in a cracked voice. "To be noticed,"

Do you hate Shinji Ikari?

Asuka shook her head to say no. Shinji appeared in front of Asuka. He just stood there and spoke. "Are you ready to leave yet?"

"Shut up!" Asuka yelled, still crying. "You're not innocent! You think it's funny, don't you? You laugh at how I can't even move Eva anymore!"

"Asuka," started Shinji. He was cut off.

"Why don't you shut up!" she screamed. "You're synch-ratio gets higher and higher while mine is nothing! The worst part is that you don't even care!" Asuka took her eyes off of Shinji and stared at the stage under her feet. "No one cares," she said quietly.

The time when Asuka was mentally attacked by the angel appeared in a soundless image. "They didn't do anything. They waited. I screamed…and they waited." Another image where Rei was being attacked by the sixteenth angel appeared. The second-to-last angel that had made Rei self-destruct Eva unit-00. "Then when Wonder-Girl was just barely attacked," Eva unit-02 appeared in the city. "They sent help immediately. And when I couldn't move," Shinji appeared in unit-01. "They sent him without hesitation…"

Asuka felt fresh tears fall down her face. "I'm a third place loser who sucks at the one thing I'm good at! No one cares what happens to me! I should just die!" Asuka suddenly noticed that she was in the bath tub of an old house. It was destroyed now, and the fact that she'd managed to get hot water in there should be surprise enough. She didn't even notice. "No one cares…" she droned in a low voice.

Her cloths were folded in a pile on a chair next to her. She stared above her with half open eyes. "Why am I here?" she said in the same low tone. "I should just die. No one cares." She closed her eyes.

"Asuka!"

Asuka opened her eyes. She was back on the stage. Shinji was in front of her again. "I care!" He said. "I'd miss you," He seemed upset. A few more spotlights shined on the stage behind her. Every time one flashed on, another person appeared.

"I care," said Misato.

"I care," said Asuka's stepmother.

"I care," said Hikari.

Asuka looked directly ahead of her at Shinji. She smiled a little. "Idiot," she whispered.

Asuka looked around and noticed she was in the entry plug of unit-02. "What am I doing here?" she asked. Why was beyond even her, but she pushed up on a few levers. Nothing happened. She concentrated on moving. Still, nothing happened. She almost laughed.

She looked at her surroundings outside the Eva. Everything was pitch black. She suddenly saw a large energy beam speeding towards her. She screamed something in German, and covered her head with her hands. After a few quiet seconds, Asuka looked up. The AT field stopped it. The yellow glow of the field was still there. That shouldn't have happened unless unit-02 was active.

Asuka's eyes widened. "Mother?" she whispered. She felt joy build up inside her. "Mother!" She exclaimed. The signs of the field faded away. "You've been here all along…" Asuka smiled. "I get it!" There was a glowing around her as Eva unit-02 reactivated. "I understand Mother," she said. The darkness broke away and Eva unit two leaped into the air. "You were always with me!"

Asuka was back on the stage in the chair. The stage broke away with her final exclamation and her surroundings became a white room. "I understand, Mother!"

Shinji sat at the table in the middle of Misato's apartment. The dinner in front of him had grown cold. He hadn't taken a bite of it since Misato placed it in front of him. Misato slammed the beer can down on the table after finishing the last few drops.

"Damn it Shinji!" she exclaimed. Anger was obvious in her voice. "Why won't you eat something?" Shinji just stared at the plate.

"I'm not hungry," he said.

"Don't give me that shit!" yelled Misato. Her face changed from blind rage to concern. "Please," she whispered. "I understand that you're upset. But please! You need to…" There was a knock on the door. Misato stood up and went over to the door. Shinji just continued to stare at his plate.

"Um, Shinji? Could you come here?" Misato called. Shinji sighed before standing up. He walked towards the front door. His un-enthusiasm changed to shock when he saw the smiling face.

"Asuka," Shinji said quietly. Asuka closed her eyes and smiled.

"I'm back," she said as the sounds of the night came quietly from behind her.

Okay. There's chapter one, hope you liked it. Now a couple of things: The Instrumentality part was difficult to write, hope it didn;t come out too messed up. And the first chapter is kind of serious, but it gets back into more of the light-hearted/happy mood of early Evangelion episodes during the next few chapters, then it'll go back to serious, just so you know what to expect.

Thank you for reading, and please review!