Disclaimer: I do not own the Fate franchise it belongs to Kinoko Nasu and Type-Moon.

Second Coming

Prologue

"Open your eyes."

Grey eyes flashed open, blinking rapidly in the light of high-power surgical lights overhead. The little girl was strapped to the gurney, leads taped to her skin snaking out from under her smock and into the beeping and flashing machines around her.

There were a series of clicking sounds, and the straps unlocked on their own accord, falling away and to the sides. The little girl struggled to rise to a sitting position, grimacing and whimpering at the pain that saturated her body, every nerve ending throbbing dully and fire flowing through her veins. Dark hair flowed over her shoulders, and partly-obscured a bandage wrapped around her head.

"What is your name?" someone asked, and she turned to see an older man dressed in white clothes nearby, his face blank and holding a pen and clipboard in his hands.

She thought briefly, thoughts and memories filtering through the fog that she belatedly-realized clouded her mind. The way the memories fell into place like a puzzle coming together felt right and wrong all at the same time, as though they felt real yet hollow all the same.

A man with unruly dark hair and empty grey eyes smiled faintly as he ruffled her hair with a hand.

Father…?

A cold-looking woman with short-cut dark hair and dark eyes smiled as she knelt down before her, fixing her clothes and patting her cheek while saying sweet reassurances.

Mother…?

They leave to go elsewhere, leaving her behind at the orphanage. And then…then what…fire…pain…smoke…shouts and screaming…

The little girl clutches herself at the memory, feeling the heat on her skin and hearing the shouts of the men looking for her for something her parents had done. "R-R-Rei…Rei Emiya…" she answered the man's question.

Is that really my name?

It feels…empty…just like…my…memories…

The pain was real though. As if triggered by the thought, fire lanced through her insides, and she doubled over, every nerve ending alight as though held against open flames, her insides squirming and her breathing coming hard as a cold sweat broke out over her entire body.

What happened to me?

Why are my memories like this?

Where am I? Where are my father and mother? Where is…where…

"Is that an answer or a question?" the man asked, and she looked to him and then down, her face scrunching up in concentration as she tried to bring her memories into focus. They swam out of the fog faster this time, the fog melting away as the broken memories fell into place and walling out the feeling of hollowness beyond.

Rei Emiya blinked as the pain and the hollowness faded, the latter much more slowly, and she slowly relaxed her body, her smock damp with sweat. She shivered in the cold air of the operating room. "M-my name…" she stammered out at first, and then paused to take a deep breath before continuing. "…my name is Rei Emiya."

The man nodded with approval though his face remained blank, and he scribbled down something on his clipboard. "Who are your parents?" he asked.

The woman held Rei firmly but gently, holding her up so she could reach and pick the apple from the tree. Rei turned and looked over her shoulder and beamed at her mother, who smiled back as she lowered Rei back to her level. Rei held the apple out and…and…mother…took a bite…they shared a smile, and Rei bit into the apple…mother…who…who was her mother…

"My mother…father called her Maiya…I…mother…"

The man nodded again. "Maiya Hisau…" he said, and Rei blinked. The hollowness resurfaced and then vanished as yet more of the puzzle was filled-in.

"Father just called her Maiya." She said absent-mindedly, her boding going slack as memories of her mother filtered through the fog. Tears slid down her cheeks as she wondered where her mother was, and why she and her father weren't there to…to protect…

"And your father…?"

Rei is five, and she peeks out from around the corner as her parents arrive. They have dangerous jobs, the caretakers at the orphanage say, and they travel a lot, so they can't really stay with her, and thus she stays at the orphanage. The way they act together when they arrive is weird, as though they have no interest at all, but when they see her they smile, and their eyes go warm, and everything else vanishes.

They are there, and that is all that matters.

But where are they now?

"Father…Kiritsugu Emiya…"

The man made another note, and nods in approval. "How do you feel?" he asked.

She lifted an arm up in front of her, the limb feeling heavy and lifeless, but after a moment it lightens and she flexes her fingers. She does the same for her other arm, and for her toes, bringing life and warmth to her legs. She rubs her arms and looks back at the man.

"It hurts." She said. "Except that…everything is fine."

The man nods and makes another note. He steps forward and places a hand on a shoulder, and Rei blinks as she smells copper in the air, and her skin tingles with electricity. An answering fire burns inside of her.

Magic…her parents could use magic too.

Their job had to do with magic too. And they had died for it.

More tears welled up and trickled down her cheeks, and she choked back a sob. Her parents were dead. She was alone now, would never see her father smile at her, or feel her mother's arms around her ever again.

It hurt. It hurt more than the pain throbbing through her entire body. The hurt went deep, all but snuffing out the lingering hollowness in her.

"Come now, child." the man said, walking over to a nearby table and working on the glass things there. "Don't cry. Your parents are dead, but you're not alone."

The man turned, carrying a glass of dark-looking liquid in one hand. He walked closer and held it out to her. "Your sister is here." He said. "We came close to losing you a few times, but you held on. And you should keep holding on, and now that you're awake you should stand and step forward. You wouldn't want your sister to be left alone now, would you?"

Rei blinked as something inside of her responded to the word 'sister'. But the hurt wasn't so bad now. It was still there, but the thought that she wasn't alone…it felt warm and comforting, like her mother's arms. And yes, she didn't want to leave her sister alone. She knew how hurting felt like, and she didn't want her sister to feel hurt.

Sister…I have a sister…I…I always had one…didn't I…? Father…mother…oh yes…they said…different families…now I remember.

The hollowness vanished, and Rei shook her head clear and wiped at her eyes with a sleeve. She remembered now. There was father, mother…and the other mother. There was also the other girl with silver hair and red eyes in the picture father had shown her once and the promise that one day they'd meet and be friends with each other.

They were sisters after all. It was only right.

She took the glass, and drank the medicine. It was cold and bitter, and she felt like spitting it out, but she knew she couldn't. And after a while, the pain began to go away, her body feeling…normal.

The man nodded and took the glass, and made a gesture while walking away. Two women with silver hair and red eyes walked over, one pushing a wheelchair which the other lifted her into after disconnecting her from the machines, and then they wheeled her out of the room.

"I still say that we're taking an inordinate amount of risk with that child." The younger magus said as he sought to keep up with the long strides of Jubstacheit von Einzbern.

"Kiritsugu Emiya was a fool." Jubstacheit replied. "But he was by no means weak. He might have betrayed us in the end for a delusional reason no doubt brought about by what happened to that doll, but he came closest to achieving our goal of attaining the Grail for us. No, I would appropriate that strength again if I could."

"We've spent two years putting that…girl back together." The other magus persisted. "Organic replication…horizontal gene transfers…marrow transplants and blood transfusions…proto-geometric mental reconstruction and more…and when she wakes up the results are still less than our optimal predictions."

"But she has woken up." Jubstacheit said. "And she has Kiritsugu Emiya's fire and earth elements, along with compatibility with the Emiya Crest. The loss of her original gift is regrettable, but it was predicted and ultimately of no concern so long as we reclaim the power of the original Magus Killer."

"And if she falls to the same delusion her father fell into over Illyasviel's inevitable demise? What then…?"

"Leave that to me."

"Lord Jubstacheit…" a homunculus wearing a slightly more formal uniform than most of his kind said, walking up to them. "…we have confirmed that the Emiya Crest – minus the parts lost with Kiritsugu Emiya – is in the custody of the Clock Tower. Our agents report that attempts to access much less retrieve a portion of said crest, has been blocked on all fronts and will require additional effort and resources to succeed."

"Damn bureaucrats…" Jubstacheit cursed before turning back to the homunculus. "…inform our agents and representatives to do what must be done to retrieve an equal portion of the Emiya Crest to that possessed by Kiritsugu Emiya. See to it personally oberstleutnant, once we have it we are a step closer to ensuring that there will be no one to stop us this time."

"Yes my lord."

Illyasviel 'Illya' von Einzbern honestly didn't know what to make of the other girl in the room – apparently they would be sharing the same suite from now on – nervously fidgeting and playing with the hem of her skirt. She was dressed similarly to Illya, with a purple, long-sleeved and collared blouse and a cravat in a lighter shade of purple over a white skirt. The difference of course was their eyes and facial features.

Illya looked like her mother did, down to the silver hair and crimson eyes. Rei Emiya on the other hand resembled her mother, except her hair was longer and instead of Maiya Hisau's brown her eyes were Kiritsugu's grey. Apart from that…Rei was slightly taller than Illya.

Not that she would ever admit to that…at least not aloud.

"Um…" Rei began hesitantly. "…I'm Rei Emiya. Nice to meet you…"

Illya wanted to be angry and jealous that she had had a secret little sister. She had wanted to be angry because it meant that her papa had cheated on her mama, and had wanted to be jealous that she had had to share her papa's affection. And she was, at least at first.

Grandfather had told her of how Rei had been hidden away in an orphanage by her parents, and how shortly after the previous war agents of the Archibald – still seething from the destruction of their crest at the hands of Kiritsugu Emiya (something which the Einzbern had no problems with despite having declared Kiritsugu persona non grata) – had burned it down and tried to kill her. It didn't work as planned, and she'd survived, but was left at near-death.

The Einzbern which had been planning on taking custody of her and training her to support her half-sister in the next war had been forced to put her back together, and it had taken two years to do so considering the amount of damage she had taken. And now the sisters faced each other.

Illya couldn't be angry or jealous of her sister. She just couldn't. Once she had heard her grandfather's story, she quickly realized that Rei had been abandoned by their papa just as much as she (Illya) had been. They'd been thrown away, Illya to rot and Rei to die, so papa could be with that Shirou boy in Japan.

Illya was many things, but she wasn't greedy. And she was lonely. The idea that she didn't have to be lonely anymore was very enticing. She could afford to share in punishing Shirou for stealing their papa's love if it meant not being lonely anymore.

Illya smiled and took Rei's hand. "Hello." She said. "My name's Illyasviel von Einzbern and it's nice to meet you too. Oh and you don't have to call me by my full name, just call me Illya."

"Illya…?" Rei echoed.

"Yes!"

"But…you're older than I am. Is it really alright?"

"Oh don't worry about that!" Illya said, pulling Rei along deeper into their shared set of rooms. Grandfather had made it clear that both would have plenty of training to come, but for today they were free to 'bond' with each other. "We're sisters aren't we? Then we don't have to be so stiff and formal with each other! Now come on, let's have some fun!"

Rei blinked as she tried to keep up with her sister, and then she felt her lips tugging into a smile. Yes, that sounded nice.

Having a sister felt very nice indeed…

A/N

This idea's been kicking around my head since the weekend (distracting me from college BTW), specifically the question: what if Kiritsugu Emiya was still alive and full-powered when the Fifth Holy Grail War begins?

Stomp…which is why instead of Kiri (the presence of whom in such a state would be utterly nonsensical (like some fics with Irisviel still alive at the time of the fifth war) considering the plot of Fate/Zero) we have his and Maiya's daughter (who would have less experience than he has). But…! Hold your horses, I'm not finished yet…there's more to Rei Emiya than what I've shown in this chapter (kukuku). It'd be boring if everything was cut and dried right from the beginning after all.