Prologue

When Shinji Ikari woke up, the first thing he saw was the hospital ceiling overhead. The sight of it always made him depressed, since it always meant that he had just come from battling an angel in Unit One. Shinji thought and tried to remember why he was here this time, since his memory was a little fuzzy.

Suddenly several images flashed through his mind. The Fourteenth Angel entering the Geofront despite NERV's defenses; the head of Unit Two crashing into the shelter he had been hiding in; Unit Zero sacrificing with N2 mine to attempt and destroy the target; Unit Zero enveloped in a bright light as the mine went off; the angel slowly advancing past the still body of Unit Zero…

That's right! Shinji thought. Asuka! Ayanami! Are they alright! I must have defeated the angel if I'm here, but are they all right?

"You are awake," a voice said, and Shinji turned to its blue-haired owner, who was sitting in a chair to his left.

"Ayanami!" he said. "You're all right!"

Rei looked at Shinji, happy for his concern, but she didn't let it show on her face. She never did, but she had been finding it harder and harder to contain her emotions around Shinji. She remembered that Shinji's friend, Suzuhara had told her that she had a thing for Shinji. Although Rei was ignorant to most thing, she knew from what she had over heard from other students that it meant she loved Shinji. She was sure, but she thought that Suzuhara was right. She hadn't been able to stop worrying about Shinji when he was absorbed into Unit One.

"Yes, I am fine." she said.

"What about Asuka?" he asked. "Is she alright too?"

"Pilot Soryu is well," Rei said, feeling a twinge of… something. She did not like it that Shinji was worried about the Second Child as well.

Shinji sighed in relief. "That's good," he said. "What happened? I can't seem to remember anything after I saw the N2 mine explode…" Suddenly, Shinji remembered something. He sat up, leaned over and grabbed Ayanami's shoulders. "Why did you do that!" he asked. "You could have died!"

Rei was momentarily shocked by Shinji's uncharacteristic outburst. She was confused when she saw the fear and anger in his face, and the tears beginning to form in his eyes. "It was the only possible way to defeat the angel," she said, and then she looked away from Shinji's gaze. It made her feel… odd. "And I can be replaced."

"No!" Shinji shouted, and Rei looked back to him. "That's not true!" he said, tears flowing openly now. "You can never be replaced!"

Rei was at a loss. She found herself unable to tell him that she had wanted to protect him, even at the cost of her life, and that she could in fact be replaced. For some reason, however, his worry made her feel strange. Perhaps it came from "having a thing" for him. "I…"

"No one can be replaced," Shinji said, cutting her off and dropping his head. Tears fell from his face and onto the bed. He had been so worried, and now she said that she could be replaced? Of all the things Shinji had to tolerate, he couldn't stand Rei thinking that way! Shinji had really liked Rei ever since he had helped from her entry plug after they had defeated the Fifth Angel. That was when he had begun to have feelings for her; feelings that had grown the more time he spent with her and got to know her better. "No matter what you think, no one can be replaced. Your life means more than that!" He looked up at her. "Even if someone brought you back by cloning you, it wouldn't be you! There is only one you!"

Rei was shocked. She didn't know what to say. For the majority of her life, she had grown up hearing the Commander tell her how she could be replaced, telling her how her life didn't matter because of what she was. But now Shinji was telling her exactly the opposite, saying that her life was as important as anyone else's.

"Ayanami," he said. "Don't ever do that again. I can't remember much after I saw the explosion, but I'm sure the reason I went back to Eva was to try and save you. So, no matter what, don't do that again. I don't want you to die."

"Ikari…" Rei said. She really didn't know what to say. This was the first time anything like this ever happened to her. After a few silent moments, she nodded and said, "I understand."

Shinji smiled and removed his right arm from her should to wipe away his tears. "Good," he said. The he noticed the position he was in. Quickly letting go of Rei's shoulders, Shinji leaned back onto his bed. "I'm sorry!" he said, reverting to his usual self. "It's just… I just…" he stuttered.

"It is all right," she said. "I am… happy you said those things."

Shinji stopped stuttering and froze. Did Rei actually say that she was happy about what he had just said? "Really?" he asked.

Rei nodded. "Ikari," she said. "Do you not remember what happened after you got into Unit One?"

Shinji shook his head. "No," he said. "I don't."

"You defeated the angel," she said. "However, when they tried to retrieve you from Unit One, they found that you had been absorbed into it."

"I was…" Shinji said, trailing off, unable to comprehend what Rei had just told him.

Rei nodded.

"For how long?"

"Thirty-one days."

Shinji just stared at her.

Rei stood up. "I must leave now," she said. "I have tests with Dr. Akagi soon." She walked to the door. "Ikari," she said, stopping at the room's threshold. "When you are out of the hospital, I would like to be in your presence more than I am now." Then she left.

Shinji just sat there in shock.

Dr. Ritsuko Akagi paced back and forth down in Central Dogma. Her lab coat spread out behind her as she continued to walk from one end of the room, to the other. She was irritated.

Rei was late.

For one thing, Rei was never late and that irritated the doctor. For another, she didn't particularly like the doll and that just made it worse. Why did she have to care for the little wench? Why did he care more for the blue-haired, red-eyed doll than he did for her? In her irritation, Ritsuko bumped up against the wall, causing the remote control in her pocket to be accidentally pressed.

Ritsuko was slightly startled when the walls began to rise around her, revealing the tank that they concealed. The tank that held LCL—and Rei's clones.

Her surprise quickly turned to anger as she stared at the dozens of pale faced, red-eyed, blue-haired copies of the pilot of Unit Zero. She hated the dolls floating there, with that blank expression. She hated the ghostly giggling that they emitted. These soulless dolls… she hated them! She hated them and she hated Rei! Because they were here, Rei would never go away! She would never have the commander to her self. She didn't know how many times she had seen him come down here in secret, staring at the Reis. They should all be destroyed!

Without realizing what she was doing, Ritsuko pulled the remote control from her pocket. Yes, she thought. They should all die! Then he'll be mine! Ritsuko pressed a button on the remote control.

Red lights flooded the room, and the blank smiles on the faces of Rei's clones changed into looks of pain, their giggles became screams of pain, and they began to dissolve into the LCL

Yes, Ritsuko thought. Die, die, die, die, DIE! "DIE!" she screamed at them, shaking her hands, insane delight plastered all over her face.

Suddenly, the giggling returned, and Ritsuko delight drained from her face, as she watched Rei's clones begin to regenerate their lost body mass.

"No!" Ritsuko said aloud. "This isn't possible!" She jammed her finger down on the control again. They needed to die.

This time, the giggling grew louder, and Ritsuko's pounding on the remote control slowed as she watched the changes taking place before her, horror appearing on her face.

Rei's clones no longer had a blank expression. They were smiling, still, but now the smile struck fear into Ritsuko. She didn't know why, they still had the same, soulless eyes, but… all the eyes were fixated on her. Ritsuko slowly backed away from the tank. The laughter from the clones now had a chill to it that it hadn't before.

Suddenly Ritsuko heard a thump behind her, and she whipped around to see that there was a clone staring at her from the other side of the tank she had bumped up against. It was staring straight at her. Ritsuko watched as it lifted an hand and then pounded a fist against the edge of the tank.

Ritsuko slowly backed toward the door. The clones had never acted like this before. They had only floated there, smiling, but now… now they were moving on their own.

Ritsuko watched in horror as all the clones swam up to the wall of the tank, pounding against the wall. They were trying to get out.

Ritsuko felt her pulse rising, and she tried to calm her self. It was fine. Though this was abnormal, the clones couldn't escape the two-foot wall of bullet proof glass.

That was when a crack appeared in the glass.

Ritsuko opened her eyes wide. No, this couldn't be happening. The red light began flashing, and Ritsuko looked to the computer display on the wall. The tank was being eaten away from the inside of the tank for no apparent reason. This can't be happening! Ritsuko thought. She was scared, more than she had ever been before. Ritsuko began jamming her finger on the remote control again, trying to destroy these… things before they escaped.

It had no effect, and all the clones had gathered around the crack that had appeared, and they were all banning on the glass, and each and everyone had on a feral grin and their eyes were locked on Ritsuko.

The LCL began to leak from the tank, and Ritsuko ran from the room, shutting the door behind her. Not pausing a moment to rest, she began to run as fast as she could.

She had programmed the MAGI. She knew what would happen as a result of this event. She needed to get out of here, now!

Ritsuko ran. Fast.

"What the hell is going on? Is it an angel?" Misato yelled as soon the alarms went off. The purple haired major had just gotten a can of beer as she entered the faculty lounge in NERV when a red light began flashing and a klaxon appeared.

"I'm not sure, Major," Maya said as her fingers ran over the keys in front of a computer terminal. "The MAGI aren't telling me anything!"

"Well find out what is happening!" Misato yelled, before turning to the other two workers who had just stood up.

"Aoba, Hyuga," she said, pointing to them.

"Yes, Major?" they asked.

"Get to your stations, quick!"

"Yes!" they yelled and began to run for the door.

"Wait!" Maya said, her eyes widening in fear as she looked at the computer display in front of her.

"What is it, Maya?" Misato asked.

Maya turned to Misato, pale faced. "The MAGI have detected contamination in Central Dogma," she said. "NERV is being locked down in attempt to contain it. If we don't get out of here now, we'll be locked in!"

Misato's face-hardened. "You three," she said, "get out of here now!"

They ran, but Hyuga hesitated at the door.

"What about you, Major?" he asked.

"I'll be right behind you," she told the technician.

Hyuga hesitated for a second, before nodding. "Alright," he said. "Just make sure you get out of here, Major."

Misato smiled. "I will," she said.

Hyuga nodded, and then began to run.

Misato turned to the computer terminal. She needed to warn everybody, now. Pressing a few buttons on the control panel, Misato began to speak.

"This is Major Katsuragi," she said, her voice broadcasting throughout NERV. "There has been a contamination in Central Dogma! All personnel, Evacuate. I repeat, all personnel, evacuate!"

The commander stood up in his office, after hearing the Major's broadcast. The flashing red light accented his hard features and reflected off the pair glasses he wore. This was most unfortunate.

"We must evacuate, sir." Fuyutsuki said. The older man saw the commander—his former student—tighten his white gloved-hands into fists. This could ruin everything that the commander had been working for.

The commander began walking toward the exit, clamping his hands behind his back. "As soon as we are out," he said, "I want a temporary headquarters set up, and find out the cause of this."

"Yes, sir," Fuyutsuki said as they stepped into an elevator taking them to the surface.

The commander stood silently. The amount of rage contained within was so great that it began to show on his face. If his plans failed as a result of this, whoever caused it would pay dearly.

Rei had just stepped through NERV's high security doors when she noticed the red alarm light flashing. Something was wrong. She turned to leave, and swiped her card through the reader in attempt to leave. The door didn't open. She tried again, and still got nothing. Something was defiantly wrong. Turning around, she went to find another way out of headquarters.

As she came to the hallway, she watched as the multiple blast doors began sealing it off. Turning, Rei ran in a different direction to try and find another way out.

Suddenly, gas sprayed out from the walls. Rei did her best to hold her breath, but she began to feel woozy. The strength in her legs buckled, and she fell to the floor.

As she slowly faded from consciousness, Rei felt despair. She didn't know why, but something about this scared her. She didn't want to leave Shinji now…

For a moment, she felt something tingle in her abdoman, and then she lost consciousness.

Shinji was feeling real happy after his conversation with Rei. She had promised to stay alive, and although he hadn't actually come out and said it, he had come pretty close to telling her exactly how he felt about her. Maybe there was hope for him yet. And she has said that she was happy to hear his words!

Suddenly, Shjinj felt a shiver run down his spine. He didn't know what it was, but it gave him a bad feeling. He shook his head. He didn't want to be feeling bad after talking to Rei, especial after she said that she'd like to spend more time with him.

He was sure that she hadn't meant anything by it. After all, there was no reason for her to like him, but it was nice to know that she was opening up more, and getting away from his father.

Shinji fell back onto his pillow. He was tired. It must have been really tough being inside Unit One for so long, though Shinji didn't understand why. He needed some more rest.

Unfortunately, events that would leave Shinji unable to rest for a very long time had already been set in motion.

Author's Note:

I will most likely re-write this chapter at a later date, partly because I didn't how some bits were worded, and partly because the chapter was too short for my liking. I just wanted to at least start writing this idea so I wouldn't keep putting it off. Anyways, on tothe Angel's Heart Chapter 8!