Prologue: The Beginning

The thing about ShinRa and it's secrets was that it was hard for anyone else to figure out what the truths were. ShinRa Inc. had twisted so many truths together like knots, that it was hard to untangle them. It was even more difficult for some of the workers who had a conscious and didn't like what they did sometimes. That was how it was for Dr. Ryuu, a third class scientist.

Dr. Ryuu was a well known scientist in the ShinRa Inc. A lot of people had respected him, even though he was related to a man who everyone believed to be a mad genius. No one could really see how the two were related either. True, they both had a deep love for science, and they had always been competing against one another to prove who was the better scientist. Of course, things really never went Dr. Ryuu's way. Especially when his brother had always caught the President of Shinra's attention with his most inhumane experiments. He was very sure that President Augustice was just as mad as Professor Hojo. Both of them were definitely power hungry. Yet, while the President used money as his power, Professor Hojo used his science. He had come up so many experiements that were definitely from the mind of an insane genius. He had used some of the most unusual methods that didn't just agree with Dr. Ryuu. And that was why he started his own project, that he knew he wouldn't agree with later on. But if it was the only way in stopping Professor Hojo from doing one of the worst things in history, so be it. And that was what he did.

Unfortunately, he had grown too attached to his own experiment. Earlier before he had started the project, he and his assisstants had been studying the immortal life. They were trying to figure out how to create a warrior who could die yet be reborn. An immortal warrior.

Of course, Dr. Ryuu knew it was impossible to create such a being. There was no way to create a fighter who could die yet be reborn. The only way of doing that was to use Phoenix downs or life spells all the time. But that was not what Dr. Ryuu wanted. Or his helpers. They wanted to create a being who didn't need curative spells or life saving items. They wanted the warrior to do it on their own. That was why they started studying the mythical creature, Phoenix.

Everyone knew what the Phoenix was. There had been a rumor that the Phoenix was once a condor from Fort Condor. And that was why ShinRa Inc. kept badgering the people at the Fort for a single condor egg. That, and because of the Huge Materia that was hidden inside it. Dr. Ryuu had even went to ask the people if they would allow him to study an egg. He had promised that no harm was going to come to the baby. However, the people refused once again. None of them trusted any ShinRa Inc. workers no matter how polite they were. The good doctor, Ryuu was not happy with the refusal but tried to find a way around it. He was not one who gave up very easily. He only found other options of continuing his research.

However, again, he didn't guess that Professor Hojo had been watching him very closely and had been reading his work. The Professor had decided to give Dr. Ryuu a small 'helping' hand by having someone steal a condor egg from Fort Condor. Once he had it, he gave it to his brother, Dr. Ryuu so he could continue his research. Of course, Dr. Ryuu was not impressed that Hojo would do such a thing but he kept quiet and continued the research.

The first half of the experiement lasted for a year until Dr. Ryuu had a break through. He had been the first to create ShinRa Inc.'s very first Phoenix Demon. They had used the condor that had hatched from the egg and large amounts of Mako energy. Professor Hojo had even been 'kind' enough to borrow a sample of Jenova cells to Dr. Ryuu. It wasn't like him to be so generous like he had been but Dr. Ryuu was too excited to see his mad brother's true intentions. He continued his research without stopping to think of what could have happened.

A few months had passed and the Phoenix had grown quite nicely. That is until Hojo decided to take over Dr. Ryuu's work as Head Scientist. There had been a huge arguement over that one. Dr. Ryuu had complained of Professor Hojo's trechery and how he was only trying to steal his work. To cover things up, Hojo had made Ryuu into his personal assisstant so they would work along side each other. Ryuu didn't like it but he didn't say anything about it. It was either to work as Hojo's second man or find another job that didn't have anything to do with ShinRa Inc. And because he was already so far into his project, he couldn't refuse the job. So he worked under Hojo's orders.

Unfortunately, Hojo had been way too hard on the Phoenix. He was pushing to hard and was trying to speed things up. The bird became ill and finally died.

The most interesting part about it though was it didn't exactly die as normal things would have. It remained in a spirit form. It was exactly what everyone had wanted it to be. The real research began then. And Dr. Ryuu did not like what was going to happen. In fact, he was totally against using humans as experiments. It was against his own standards and it sickened him when Hojo had chose his human experiement for the project.

A young girl.

Dr. Ryuu stared into the window of the cell where they were keeping the girl. He felt incredibly sorry for her. Especially on what was going to happen to her. She was a pretty little thing and he couldn't help but feel very protective over this child. It just disgusted him when he found out where they had gotten the child.

She had been kidnapped years before she was brought to the secret lab near Nibelhiem. She had been taken by ShinRa SOLDIERs, who had destroyed a very small town near Wutai. It was right after the war against Wutai. The town had only been at least 20 miles away from the village and that was where they had taken the girl. General Sephiroth had personally seen to it that she was kept alive and hidden away from some of his men. Dr. Ryuu had learned from the silver haired young man that some of his men had tried to bully the girl several times during the war. The girl had been only six years old then. While the ShinRa army had literately destroyed every single person in the town on the island, Sephiroth could not see this girl being killed. And now that Dr. Ryuu was looking at the girl, he could see why.

She may have been very young, but she was one of the most beautiful young girls he had ever seen. Her hair was coal black and she had deep ivy-green eyes. She was a small and fragile looking thing but there was strength in her eyes whenever she looked at anyone. She would always glare at someone, daring them to even touch her. Dr. Ryuu was already growing fond of the girl.

During the long weeks of her stay, Dr. Ryuu was allowed to be in charge of the girl. He was to look after her and make sure she had everything she needed. He had spoke to her many times before but had never really learned her name. And when he did ask, she didn't know what her name was. She believed her parents had called her Eden. And so that was what she was called. Only everyone called her the Black Beauty. One because of her beautiful black hair and two because she was a little beauty. Dr. Ryuu then named the girl, Eden Black.

He was growing quite close to Eden, as was the Phoenix. They had tested the demon's reation to her and it had shown a liking to her. The Phoenix demon was quite protective over her while she was staying with it. It would not allow anyone other than Dr. Ryuu near her while she was in it's cell. It seemed to like only the doctor other than Eden. And that was what made him even more upset about what they were going to do now.

The next step to the Phoenix Project.

Dr. Ryuu sighed as he watched the young 12 year old reading her books like she had been told to. She was learning quite a lot now. And she proved to be a fast learner. During her years of staying in the lab, she had been tested many times. She had been instructed to read as many books as possible. Most of them were arithmatic and science books since that was mostly what they had in the lab. She was always reading education books and was becoming a very bright young girl. She was also exercising all the time. Professor Hojo had told the good Dr. Ryuu to make sure she was in top physical shape. She was quite strong for her age as well. She had even had a few Mako injections, which was not pleasant for the girl or Dr. Ryuu. The doctor could never stand listening to the girl screaming in pain when she was injected. He also had always wondered why Professor Hojo wanted Eden to exercise so much and become very strong but he had never asked. Like always, he never stopped to think. And it was only that morning he discovered what Professor Hojo had in mind.

The kind doctor sighed again before he decided it was time. He had been ordered to take the girl to the other side of the lab. It was time to begin phase two. He knew that Eden would never forgive him for this. He knew that he wouldn't forgive himself either. He didn't think he ever would.

Dr. Ryuu shook his head as he placed his palm against the hand lock to open the door. With a hiss and a beep of access granted, the door slid open. Eden looked up and faintly smiled at the doctor, who returned the smile.

"Good morning, Eden." Dr. Ryuu said gently as he walked over to where she was sitting.

Eden nodded. "Good morning, doctor." She then frowned. "Please don't tell me that it's time for my shots." She sounded almost like she was pleading.

Dr. Ryuu frowned looking saddened. "I wish I could say that it wasn't that time, but it is. I'm sorry you have to go through this so much, Eden. I have tried several times to get Professor Hojo to not do it and to release you, but he will not hear of it."

The young girl sighed closing her book before standing. "I know, doctor. I know your just trying to help me. I'm afraid that no one can now." She said. Dr. Ryuu shook his head as he gently placed his hand on her shoulder. "Now, now, Eden. The only one that can actually help you is yourself. You must be brave and strong for all obstacles. No matter what they be. Don't ever give up hope, do you understand?"

Eden smiled at him and nodded. "Yes, Dr. Ryuu."

Dr. Ryuu nodded towards the door. "Now, let's go get this over with and then you can rest for an hour. After that, I'll let you go see Phoenix." Eden's smile grew wider and she allowed him to lead her out of her room.

He frowned as soon as they were half way down the hall. He really wanted to tell her the real truth. But then again, he didn't want to see the fearful look on her face more than she usually had. He knew that she was dead scared of Professor Hojo and he couldn't blame her. There was just those things about his older brother that made him shiver. He had heard a few rumors that Hojo had did a few experiements on himself that could alter him incredibly. He could only hope that they were only rumors and not the truth.

They finally reached the lab where her life would really change. Eden had looked around the lab as they walked in before looking up at the doctor. She could already see that he was not happy about something. And she had a feeling that what she was doing in this particular lab, she knew she wouldn't like it. But she was going to try to be brave no matter what Professor Hojo had in store for her. She was going to be the little warrioress Dr. Ryuu believed that she was. She was not going to let Professor Hojo scare her. And speak of the devil, here he came. He was being followed by one of his assisstants. The assisstant was carrying a tray with a few needles. Eden didn't like the look of where this was going. She only had to be injected with Mako once a week with only one needle. But why was she going to be injected with three needles? She didn't like this.

Dr. Ryuu saw the uneasiness in Eden and he pitied her already. He gently placed his hand on her shoulder and gave it a light squeeze of comfort.

The young girl just looked up at him and faintly smiled. "It'll be all right, Eden." Dr. Ryuu softly spoke to her before looking sternly at Hojo. "Remember our agreement, Hojo."

The Professor just smirked coolly at him. "I remember, Ryuu. But have no fear. This won't take too long." His black eyes looked onto Eden, who shrank away from him. "You, girl! Sit on the table." he told her rather demanding.

Eden gave him a cool look but didn't move. Professor Hojo looked like his temper was starting to rise. His cruel smile faded and he glared at her. "You better do what I tell you or there will be consequences." He warned darkly.

Dr. Ryuu gave his older brother a cool look before gently pushing Eden towards the table. "Hojo, you really need to learn how to treat children. Come, Eden."

Eden allowed him to lead her to the table and help her get on it. She just sat there waiting for further instructions. Dr. Ryuu reached over and took one of the needles from the assisstant. Inside the tube was clear liquid. "Eden, you may want to lay down for this one." He told her. Eden nodded and did what she was told. She just laid there as another assisstant rolled up her sleeve. Dr. Ryuu prepared to inject her, pausing only for a minute. He smiled down at her as he used his free hand to push her bangs back out of her green eyes. "Eden, I'm sorry." He whispered before he injected her with the needle.

Eden just gave him a confused look before she felt very tired. She closed her eyes and fell into a deep slumber.

Dr. Ryuu sighed and shook his head as he put the tranquilizer down on the tray. "All right. Let's get to work."

Everyone nodded and began to move around. Dr. Ryuu stayed right by Eden's side looking down at her as she slept. Professor Hojo was having an assisstant roll a large tank towards the table where Eden was sleeping. Inside it was what looked like a live flame. And as soon as it was close enough, a head formed inside the flames. It was the Phoenix Demon. And it didn't look happy at all. It began screeching and making quite the racket.

Dr. Ryuu seemed to guess what was wrong. He held up a hand. "Don't worry. She's only asleep, Phoenix." He spoke to her. The Phoenix slowly stopped screeching.

During the proceedure, Eden had whimpered once or twice in her sleep as the two scientists continued their work. Dr. Ryuu had a worried look the entire time. He wasn't happy that they had to do this to Eden. But he did have his orders. They had injected her with the original Mako liquid but also with some more of Hojo's Jenova cells. This was definitely one thing that he had objected to. He had heard what Jenova cells could do. He had spoken to Sephiroth about them once before to ask what it was like. Sephiroth had told Dr. Ryuu that it was not a very pleasant feeling. That was what made Dr. Ryuu even more worried. He could only hope that if the experiment worked, the Phoenix would be able to destroy the cells before they could do anything to harm Eden. That is if they were successful in transferring the Phoenix inside Eden. They were going to place the demon inside Eden, hoping that it would work. She would become more inhuman though. And that was had Dr. Ryuu so upset all morning. The thought of this made him shudder. The little girl he was beginning to love was going to be less and less human once they were done with the experiment. And he couldn't really bare to think of her as a monster, which was mostly what Hojo created.

Finally the last step of the experiement came. The transferring of the demon into the girl. They had attached a tube to Eden and the transfer began. Everyone had to wear special glasses to protect their eyes. When the transfer was a go, bright light filled the room, blinding those who were not wearing the special glasses. Dr. Ryuu was holding his breath, hoping that the transfer would not harm Eden.

As soon as the transfer was completed, the light dimmed and they were allowed to take the glasses off once again. To their surprise, the Phoenix had vanished from the tank. It was no where to be seen. Dr. Ryuu tucked his glasses into his lab coat and stepped closer to Eden. He halted and had to hold his breath once again when he noticed that Eden had changed quite a bit. Her usually raven black hair had turned to blood red. That was the most unusual thing that had ever happened. The kind doctor stepped closer and used a small instrument to see if it had worked. The object gave a small beep and he looked at Hojo.

"The Phoenix is inside her now. It has worked." Some of the assisstants had cheered.

But Hojo just smirked. "Very good. Now we begin the ultimate tests."

Dr. Ryuu shot him a dark look. "What ultimate tests?" He asked seriously.

Hojo smirked. "We must see if she is the warrioress we have been trying to create. She will have to fight for her life. But don't worry, Ryuu. If we really did succeed, she will only be reborn." he said. Dr. Ryuu turned to face him. His arms spread out a little. He had a very dark look on his face. "That is enough, Hojo! She is only a child! She is not a fighter! We have not taught her how to fight and I refuse to let you take her life just to see if she can be reborn!" Hojo frowned darkly at him.

"Professor, Dr. Ryuu is right. She is too weak right now." Another assisstant piped in.

"Right at this moment, she is asleep and she won't be able to defend herself." said another.

Dr. Ryuu and Professor Hojo just glared at one another before the mad scientist turned sharply away. "Very well! We will not start the tests now. We will wait for three days before testing her." He said. Dr. Ryuu shook his head. "Hojo, she will not be ready." He said stubbornly. Hojo jerked around. "All right, Mr. Smartypants! When do you think she will be ready?!" He demanded.

Dr. Ryuu continued to glower at him."Not any time soon. If she is to fight for her life, then she should be prepared to do so. She will need to learn how to fight."

Professor Hojo thought for a long moment before nodding. "Very well. Prepare her. And as soon as she is ready, she will be tested." He then stomped out.

The low class scientist gritted his teeth as he cursed Hojo inwardly. He closed his eyes trying to calm himself before he turned to Eden. He looked her over before softly smiling. He gently brushed her bangs out of her eyes. "Dear precious Eden. I will make sure that you will be ready." He whispered. He turned a glare over his shoulder at Hojo's retreating form. "Even if it kills me."

The days slowly went by. Eden had not been happy when she found out what had happened to her. She had refused to speak to anyone for a few days. Dr. Ryuu didn't blame her for being angry. He was angry himself. Angry at what he had done and at Professor Hojo for even considering it. The days turned into weeks and that was when Eden's real training had begun. She began to study the martial arts and other different kinds of hand to hand combat. She learned them pretty fast. Her senses had enhanced greatly now that she had the Phoenix demon inside her mind. She could see, smell and even hear better. Her reflexes were even faster. The only thing that it didn't enhance was her strength. She was not as strong as Hojo had wanted her to be. But she did prove to be one of the most strongest girls there was. And she was only getting stronger when she exercised daily.

After a year of hand to hand combat training, she began learning weaponary. She was taught how to handle all sorts of weapons. She favored guns and swords the most. But no matter how much she asked, she was never given one to keep for outside training schedules. None of the scientists wanted her to have a weapon in her possession just in case she wanted to escape. She grew quite marvalously throughout the years of her living in the lab.

She was now becoming a full fledged young woman. She had cut her hair short so it wasn't always in the way while she was training. She cut it to her shoulders in a layered style and she even had small golden metal rings braided in her hair for her own different type of style. The clothing she favored was black. When she turned fourteen, things really got ugly.

There had been word from the surface that things had gotten out of control for ShinRa Inc. No more than a mile from the lab, so Eden had heard, that the great General Sephiroth had lost his mind when he found out that he too was an experiment created by Hojo. He had destroyed the entire town of Nibelhiem. Luckily for the hidden labatory, he had forgotten about the lab and just passed by it when he headed into the mountains. After word came that Sephiroth had been killed, Hojo had grown quite angry and became much more insane in his science. Several times, Eden had heard Hojo arguing with Ryuu about starting a new project with her. She had overheard him saying that he wanted to combind another project with the one the one that she was on. Some kind of project called Jenova Project. Just by hearing that name made Eden shiver. She didn't like the sound of it and neither did Phoenix. She had learned that she could talk with Phoenix whenever she wanted. And Phoenix had learned that if she wanted to, it could take control of Eden's body for herself. But out of the friendship the two had created together, it never did it.

Finally after two more years, Hojo had given up on the Phoenix Project. He began working on something else so Dr. Ryuu was put back in charge with the project, much to Eden's relief. They were much happier to know that Hojo had no longer had interest in Eden. He had even forgotten about the tests that she was suppose to go through. And for the first time for many, many years, she was allowed to go to the surface to see what the world looked like because she had forgotten.

Dr. Ryuu, of course, had to be with her at all times. She never tried once to escape, even though she was strong enough to do it now. She liked being with Dr. Ryuu. He was like a father to her and she was a daughter to him.

Two more years passed and she had reached the age of 18. Hojo again began badgering Dr. Ryuu about having Eden be apart of the Jenova Project. Once again, Dr. Ryuu refused to let him experiment on Eden.

"Why do you want to use her anyway?" He asked after Hojo's fifth time on badgering him. Hojo wouldn't say though. He just snapped, "It's none of your business!" and then went on his own way.

Dr. Ryuu soon found out why. News had reached the hidden lab that Sephiroth was still alive and was causing havoc above. There had been a group that called theirselves Avalanche that had been defying ShinRa Inc. and were also trying to destroy Sephiroth. And the reason why Hojo wanted to be put in charge of Eden was because the new president of ShinRa Inc. was going to pay a visit to the hidden lab. Everyone was quite excited that President Rufus was going to visit. They had not had a visit from the President for such a long time. Eden had never got the chance to meet the former President, not that she had wanted to. Dr. Ryuu had told her so many things about him and she hadn't liked the sound of him at all.

The visit soon came. Eden had been sitting her cell doing her reading when she heard some kind of commotion outside her room. She looked up towards the window and saw a few people running back and forth. She just shrugged and went back to her reading when there was a tap on the glass. She looked up once again to see who it was and paused.

There standing at the window was a young man staring in at her coldly. Dr. Ryuu was standing next to him and seemed to explaining something to him. The young man was quite handsome and he wasn't very much older than Eden. He was at least in his early twenties. Eden figured he must have been at least 21. He had slicked back strawberry blonde hair and the coolest blue eyes she had ever seen. He wore white suit with a black turtle neck shirt under the jacket. He had the look that he had never smiled or laughed in a day of his life. There was just something about this young man that Eden didn't seem to like that much.

True, he was the very first young man she had ever seen but he looked not too friendly.

Behind him was a few people. A short but fat man in a mustard yellow uniform was peering in the window looking at her with interest. While a skanky woman in a tight revealing red dress eyed her in disgust. Eden frowned as she tried to use her enhanced hearing to hear of what was going on outside her door. The words weren't very clear but it didn't take a moron to figure out that the conversation that Dr. Ryuu was having with this young man wasn't a very friendly one.

The young man finally looked away from Eden and gave Dr. Ryuu a very cold look. He didn't look very happy at all. In fact, he looked like he was shouting.

Eden immediately disliked this man for shouting at Dr. Ryuu.

She closed her book and watched the people outside her cell for the longest time. The blonde young man was continuing talking with Dr. Ryuu, who now had a strange expression on his face; a very thoughtful look. He then nodded to the man and looked back at Eden through the window. He gave her a very faint smile, who slowly returned it. The blonde young man had glanced back at her before turning and walking out of view.

Eden found out later that night of who the young man had been and why he had been yelling when Dr. Ryuu had made his visit. They ate dinner together in Eden's room as Dr. Ryuu explained.

"The man you saw earlier happens to be President Rufus Shinra, Eden. He's the youngest President in history. It's said that no one has ever seen him bleed or cry. He's a very hard young man and he's definitely different from his father." He told her.

Eden slightly smiled. "Oh, well that's good."

Dr. Ryuu shook his head. "Actually, not really. He may be different from his father, but he's still like him. He wishes to control the world just like President Shinra had. You see, President Shinra had controlled the world with money and broken promises. President Rufus, on the other hand, wishes to control the world with fear. He wants to force everyone to like him."

Eden tilted her head. She didn't like the idea of someone trying to control the world with fear but wanting to be liked was another thing. "Doesn't anyone want to be liked?"

Dr. Ryuu smiled and gave a slight nod. "Yes. I suppose you are right. President Rufus is just a young man. He's still young and has his own dreams. It's probably only a matter of time before he realizes that he can't force people to do anything. He must learn that if he wants to be liked, he better do it without fear."

Eden slowly nodded. She gave a shrug. "So why was he yelling at you earlier?"

Dr. Ryuu pulled a face as he thought about it. "Well, you see, Eden. He never knew about this lab. No one ever told him about it. So he was quite angry." He said. Eden tilted her head. "So he yelled at you for not telling him about this lab?"

Dr. Ryuu faintly smiled. "No. It wasn't about that. He's against human experiments. That was another thing that his father and himself could never meet eye to eye. When I explained about you and the experiments that we had been doing, he was more than angry. That was why he was yelling. He demanded that we shut down this operation immediately. And he fired quite a lot of people today."

Eden's eyes lit up. "He didn't fire you, did he?"

Dr. Ryuu gave a lazy shrug. "I'm afraid he did. But I do not blame him one bit. You see, I should have stopped this experiment long ago. I was against the experiments we did on you. And now, I have been punished. I will not complain at all about this. The better part is, you're to be set free." He told her.

The young woman's eyes lit up. "What?" She asked. Dr. Ryuu smiled. "That's right, Eden. You're to be freed. No longer our prisoner, our experiment. The President has ordered it. By the end of the week, you are a free woman. You are free to go where ever you want. No more cells, no more Mako injections or Jenova injections. No more Professor Hojo."

Eden had to smile at that one. "What about you? What are you going to do?"

Dr. Ryuu frowned. "Well, I've been called to go to Midgar for a hearing along with all of the other scientists. There, we're going to be questioned about every thing that we have done. The President will decide if we deserve to continue our work as scientists."

Eden's smiled. "I hope that you get your job back then."

The doctor just smiled at her and shook his head. "No. I would rather not. I have decided it's time to retire. If I am offered the job back, I'm going to decline." Eden just smiled.

Unfortunately, the very next day when Dr. Ryuu was called away, things really fell apart. There had been a terrible fire that night and it was said that none survived.

No one. Not a single person.

Dr. Ryuu was devastated to hear the lab had been burned down. He had learned that there was no sign of Eden. None of the ShinRa fire squad could find her body. It was believed to be incinerated. He was one very broken hearted man. He had left ShinRa aswell, just after the Weapons began attacking every where. He went into hiding and was never seen from again.

Not even after ShinRa Inc. had fallen, when President Rufus Shinra was said to be killed by the blast of the Diamond Weapon. No one ever seen or heard from Dr. Ryuu Hojo again.

There was one thing though that Dr. Ryuu had not heard about.

Before the fire, one of the ShinRa representives had been ordered to make sure that Project Phoenix was completely terminated. It was not to be known by anyone of what the project was about. Every single scientist that had been involved was to be exterminated, including Dr. Ryuu. He, however, had not been there that night so he had escaped. Everything else was destroyed though.

Before the fires broke out, the ShinRa representive was going to witness the execution of Eden Black. They were going to kill her by shooting her. However, that was when Phoenix took over.

Flames had engulfed Eden and she had transformed into a magnificent bird right before everyone's eyes. No one survived the Phoenix's wraith. Not even the representive. Only one person. And his mind had turned into mush after that. He had been scared to insanity. The only thing he had said was that a bird of fire had destroyed the lab and disappeared in thin air. No one ever saw the bird of fire. It was believed that the man who had escaped was nothing but a crazy loon. So no one really believed that anyone escaped the fires but that man.

But what they didn't know was he was not the only one to survive.