Author's Notes:
SPOILER ALERT - THIS STORY ASSUMES YOU'VE READ FATE/STAY NIGHT HEAVEN'S FEEL AND WATCHED FATE/ZERO.

Now, with that out of the way, here's what I'd put on the book jacket if this were a book.
I've always felt sorry for Matou Shinji. Sure, he's a terrible, terrible human being who caused half his failures with his own incompetence. Sure, there are a lot of characters in Fate/Stay Night in much worse situations. Sure, Shinji actively contributes to the suffering of even less fortunate characters.
OK, I'm not making a great case for him. Point is, though, he was dealt a really shitty hand in life. His only family members are an immortal monster, a father who doesn't care whether he lives or dies, and a sister who, despite being a kind and caring person herself, is nonetheless a walking symbol of the reason why Shinji's life is so fucked up. Top that off with the fact that as a child he was lead to believe he was the heir to the Matou magic until he happened to walk in on Sakura in the worm pit, at which point the rug (read: his purpose for living) was pulled out from under him and his family stopped even pretending to care about him.
Then, on top of all of that, he enters the Holy Grail War (his one and only chance at redemption) and fails immediately. He ends up being the disc one villain, there only to facilitate the hero getting stronger with his own death. No matter how much of an asshole he is, you can't deny Shinji has a terrible life.

Consequently, I was pretty happy to read Kariya's Legacy, another story on this site which chronicled the events by which Shinji enters the Holy Grail War as a magic user working to protect his sister. Unfortunately, that story has been abandoned for about two years now, and is incomplete. So I decided to do my own version, starting from the top. I didn't think a quick chat with Uncle Kariya was enough to revolutionize Shinji's whole outlook, so my version diverts there.

Prologue

Matou Kariya's mind shattered a very short time after the lack of available oxygen induced brain death in the woman he loved.

Kariya hadn't been stable in quite some time, of course. There was the horror of seeing his beloved's daughter turned into a breeding ground for worms in order to receive the Matou legacy; the pain of the similar treatment he had undergone to spread the crest worms through his own flesh, enabling him to bear a servant; the shock of being unable to best the man he blamed for his woes even after all his sacrifices; the despair at being blamed for that man's death by Aoi, for whose sake he'd been going through all this (or was it Sakura's sake? Fine details like that had been slipping from him for some time now…)

All things considered, the total leave from reality his mind took after he killed her was understandable.

Laughing and crying, muttering under his breath and barely maintaining enough motor control to do so, Kariya got up and left the Kotomine Parish, headed for his ancestral home. While the bulk of his consciousness entertained itself in the fantasy celebration of his victory and well-deserved happy ending, some small part of him that clung to the world dragged Kariya back. Perhaps he hoped to die in proximity to Sakura, at the very least. From the way Berserker was rampaging, he'd certainly be dying shortly.

Matou Shinji, seven years old, woke up with in a cold sweat. He'd been having a strange nightmare; he was older in the dream, and involved in some kind of fight. Already the details were slipping, but he remembered two other adults, fighting each other, one for him and one for [Emiya] someone he didn't know. Then there had been the terrible silver gleam, and the figure fighting for him crumpled. In that moment, Shinji had been washed away by fear, and he'd woken up. Even as the traces of the nightmare faded, Shinji clearly felt the overwhelming emotions his dream self had felt. He remembered need, the need to win more than anything, because only if he won could he [really exist] feel alright; and he remembered the despair he felt when he knew he wouldn't win, that he'd die without ever amounting to anything, never proving himself to his grandfather, never becoming a magus, never beating that annoying Fake Janitor, never triumphing over his hated sis-

SLAM

The dream, and the strange [memories] thoughts that it had brought were driven from Shinji's mind when he heard the front door being opened. It startled him, because the Matou house never had any loud noises. Even as a child, Shinji knew that very well. Someone, though, had slammed the door open with no regard for Grandfather's preferences. Despite his fear, Shinji got up and went down to see who it was. He had to know what kind of person didn't care about his Grandfather.

Still dreaming of picnics and happy families, Kariya hardly noticed as he slammed open the front door of his home with all his rapidly decaying strength. He didn't have much in the way of finesse now. What he did notice was the sharp note of a child's scream. Kariya was jolted sharply back to reality, and observed that he was in the Matou front hall. In front of him, frightened and not recognizing the strange man, was Sakura. Wait, that couldn't be right. Sakura knew what he looked like after the treatments. Kariya blinked, and realized it was another child. It was about the same size as Sakura, but the shape and colors weren't right. By the time he worked out that the child in front of him was Byakuya's son Shinji, Kariya had gotten as close as he was likely to get to a lucid state. He realized two things. First, he would be dead in a very short time. Second, he needed to say something to the frightened child in front of him.

"Whattsa matter, Shinji? Don't recognize your uncle?"

"Uncle Kariya? What's happened to you? You're all bloody, and your hair is the wrong color!"

Kariya came to another realization. Since this whole sordid affair had begun, he hadn't seen Shinji once. His mind starting to work, he further recalled that Zouken had decided Shinji was useless as a magus, and would be kept ignorant of the realities of the Matou. He'd tried to convince Byakuya to send the child away to study abroad during the war, but it was now apparent Kariya's drunken brother didn't even care that much for his tiny son. There had been a time when (a slightly saner) Kariya had considered Shinji the best hope for a future to come to his rotten family. A normal, healthy, mundane future, with a Matou leading the family in business, putting their wealth to use and engaging with the world. Kariya no longer cared about a normal future for his nephew, though; all he cared about now was Sakura, which is why he said the following:

"Sorry you have to see me like this, Shinji. I'm not doing too well. See, there's something happening in our family that isn't any good. No good at all. I'd explain it to you better, but I don't have much time left…"

At this point in his ad-hoc speech, Kariya knelt down and put his one functional hand on Shinji's shoulder, looking him in the eyes.

"Shinji, the Matou can do magic. Well, your grandfather can anyway. He didn't manage to pass the ability on to you, so they brought in another child to take it on. Your new sister, Sakura, that's why she came. They've been doing terrible things to her down in the basement for a magic ritual, so your grandfather can be even more powerful. I tried to stop him, Shinji, and that's how I ended up like this."

At this point Kariya had to turn to the side in order to avoid getting any blood on Shinji when his speech was punctuated by a hacking cough that left a sizable blood spatter on the boards.

"Shinji, I have to leave things to you. Your father and grandfather, they can't be trusted. If you care about your sister, and you don't want her to end up like me, I need you to follow my instructions. Get into your father's study when you're older. Learn as much about magic as you can. Then, when you understand what the Holy Grail War is, read this. It's everything I've written about how I tried to stop your grandfather."

At this point Kariya extracted a battered journal from his coat pocket and put it into Shinji's shaking hands. Then he turned again and added a second stain to the no-longer-pristine entryway. Tiny insects had emerged en masse from the shadows to consume the blood he'd already lost.

"You're not ready for it now, but if you start learning soon you can help her by the time you're a grownup, Shinji. Don't ever show that to your father or grandfather, though, and don't read it 'til you're older. Maybe 12? Damn, what was I like at 12…"

At this point Kariya's mind tried to wander off again to happier times. When he was a child the world had seemed like a bright place. He didn't really understand the horror of the Matou magic, yet, and just thought he had an important future and responsibility. He'd had so much hope back then...
Kariya forced his mind back into place. He really didn't have much time left, and if he died while hallucinating about imaginary happiness it'd be one more failure on the pile.

"Anyway, can you promise me you'll do that, Shinji? Promise me you'll learn magic, and save your sister, and take care of her? It'll take a long time, and it'll hurt a lot, but you're the only one who can do it."

"I understand, Uncle. I'll learn, and I'll win. Don't worry anymore. It'll be okay, so you don't have to cry anymore."

Kariya realized at this point that the capillaries in his eyes had ruptured, and blood was running down his cheeks. As a metaphor, he supposed it worked. With his nephew's reassurance in his ear, Kariya allowed himself to relax. He wrapped Shinji in a hug, thinking that in a moment he'd stand up, pat his adoptive successor on the head, and go off to die in private.

Matou Kariya died there and then, embracing his nephew.

At seven, Shinji hadn't understood most of what his uncle had told him, but a few key details had made it through. Magic was real; his uncle had been hurt badly by it, and his cute new sister hurt too. He had to learn about it, and somehow that would save her. When he'd opened his mouth to ask Uncle Kariya to explain, though, he'd suddenly been filled with the feelings of dream-Shinji. There was that overpowering need to win, to prove himself, and somehow Shinji felt like this was the moment. His chance to do just that. Shinji had accepted, and his uncle had died happy. Shinji was too young to understand death, though, so he mostly thought he'd helped Uncle Kariya rest and go to sleep. At this time of night, Shinji thought, everyone ought to be asleep.

There was one other thing that Shinji hadn't understood. The Makiri had always specialized in the control of living things, even using that specialization to craft the Command Spells that made the Holy Grail War possible. Shinji's mother had been chosen from another line specializing in interactions between spirit, od, and the body. It had been hoped that this specialization would synergize with the Matou magic and help her Inheritor sorcery trait pass Byakuya's waning magic circuits to their child. The trait itself had been passed on, but nothing more, and Byakuya's wife had paid dearly for her failure.

In deference to his family's specialty, one of the few mysteries of the Matou magecraft that Kariya had actually learned was the "Instinctive Geas". This was different from an ordinary Geas, in that it didn't require od from the bound party and acted at a subconscious, rather than conscious, level. In the hands of a master, it could be an incredibly powerful tool that allowed a magus to make people into unwitting puppets. Kariya had only ever been able to make it work on his family's blade-winged insects, though, so when he tried it on Shinji it had been a desperate last-minute gamble with the final ounces of prana left in his body not yet consumed by the crest worms or Berserker. The exertion had brought about his death, but the hastening was only by an hour or so.

A human sacrifice always empowers magecraft, and with the combined enhancing factors of Shinji's blood relation to Kariya and his verbal acquiescence to the dying magus' geas-laced request, the geas had worked. Like all biologically actualized mysteries, there was a bit of life to the geas, and it made its new home deep in Shinji's immature subconscious. There it melded with the other strong impulse within him, inserting itself at the base of Shinji's mind like chemical ore in the wellspring of a river. No thought, from then on, could flow forth without the taint of the geas on it. For the rest of Shinji's life, his mind would be dominated by three subconscious compulsions. First, he would learn magic. Second, he would save and care for Sakura. Third, he would be victorious. The possibility of these things coming to pass was, of course, doubtful. Shinji had no magic talents, and certainly no caring teacher to help him. Shinji was cruel and vindictive by nature, and that nature would twist and war against the geas' compulsion to care for Sakura. As for winning, this was the vaguest of the urges; what would he win at, and how would he do it? Subsumed by the others, that urge would remain dormant until a certain event when Shinji was seventeen.
The Holy Grail War would change everything, and it would give Matou Shinji the chance to fulfill all three parts of the warped geas dominating his mind at a stroke.

More Author's Notes:
That's it for the prologue, hope you enjoyed it enough to read chapter 1 in a week or so!
Before I let you go, though, I'd like to outline the points where this story diverges from the canon Heaven's Feel timeline and mention updates. First, Byakuya doesn't send Shinji out of the country. It always seemed odd to me that a guy who doesn't care what happens to his son decides to send him to study abroad to shield him from the 4th HGW, and Shinji's backstory in Heaven's Feel makes it sound like his whole childhood was spent at home with Sakura. So what, did he study abroad for like 2 weeks? It didn't make sense to me, so in this story Byakuya's even more of a jerk and Shinji got to stay home during the war, resulting in his interrupting Kariya on his way to jump in the worm-pit. Second, Kariya kept a journal of the events of the HGW. He spends most of his time in Fate/Zero skulking around and watching others with Berserker in astral form, so it seems reasonable that he could have kept a decent account. This is my method of giving Shinji some incomplete knowledge of the Grail War besides what Zouken deigns to tell him later on. I think everything else that happens can be rationalized as the result of those events, and I'll do my best not to divert from canon in ways that can't be traced back to those points of divergence.
The other thing I wanted to mention is that not all the chapters will be this short. It's a quick intro, but I'm working on chapter 1 now. I intend to make each chapter around 7-10K words going forward, and post a chapter once every week or two. Here's hoping you liked this, and will like the rest of Rejuvenation of a Bloodline! Please ask any questions you have in the reviews, and don't hesitate to correct me if I get details of the Nasuverse wrong.