This is a really detailed challenge. But you can disregard parts you don't like. It's just an idea I wish I had time to write. Also probably the skills, my knowledge of the Fate universe (especially Clock Tower) is slim, since I haven't watched/read material from the Fourth Grail War or Hollow Ataraxia.

1. When Kiritsugu destroyed the Holy Grail at the end of the war, the taint twisted the ensuing blaze. As a result, Shirou, the only innocent survivor, possesses the same crippling taint as Kiritsugu. Thus, despite rescuing Shirou from the fire, he was not saved.
2. Shirou experiences the fire in the same way as he did in FSN - he feels guilt for being the only survivor and feels intensely indebted to Kiritsugu. Feeling intensely guilty himself, Kiritsugu vows to try and save Shirou before he dies from the grail's taint. This involves a rather reckless and insane choice - seeking out mages for help. Reasonably, mages are the only ones who can help cure Shirou of his illness. Kiritsugu might have stood some small chance of discovering a cure, but the taint in him has left him too weak to consider performing any healing/restoration magic himself.
3. Kiritsugu tries to find aid in Japan. This could be an interesting opening arc for the story. He might meet some minor characters from Tsukihime, such as one of the doctors that looks after the Tohno family. Or, he might just try dealing with various Japanese mages, doing mercenary work as best he can in his degenerating state to purchase or win over their aid.

Kiritsugu slowly discovers that the version of taint Shirou bears breaks down the body's natural defenses, acting similar to AIDS, but it also sporadically attacks muscle and nerve groups, causing debilitating pain and temporary paralysis. Some mages that have inspected Shirou have made numerous, contradicting claims about the taint's long-term effects. Some think it will eventually target Shirou's brain or spinal cord, causing permanent paralysis, brain death, or at least, brain damage. Other mages believe it will cause malignant tumors to form everywhere in his body and spread. Others still believe the taint will turn him into a "monster".

The taint is not aggressive in destroying Shirou's magical circuits, "strangely" (the fire effected the taint's effects on Shirou, but that's to be revealed later) and instead "clogs" them, reducing their effectiveness and making his magic hard to control.

Shirou himself is taught about magical society from a young age, as Kiritsugu explains to him why he is sick. He never tells Shirou that he's terminally ill. Shirou may or may not be dense enough to figure it out himself. Regardless, when he sees his father working hard to help cure him (taking progressively worse and worse jobs, as he becomes less and less able to fight), he desires to become skillful in combat. He wants to stop being a burden to his father and forces him to instruct him/give him materials to learn from. Shirou has a distinct talent for archery and swords. His magic is wild and difficult to control, but despite the taint, he can still use reinforcement magic. Because Shirou exercises his "tainted" circuits, he is able to utilize the full 27 he was born with (unlike canon). Unfortunately, he's about the same in terms of potential, at least while he is cursed.

3. Kiritusgu is dying. He's desperate to save his adopted son and willing to forsake everything for him. Since he's practically already dead anyway and because he's exhausted Japan's resources to the point where he feels he has no other choice, he uses all the money he has accumulated to go to Clock Tower. I'm not exactly sure how this would play out, how Clock Tower would react to this situation at all (or what Kiritusgu would feel "giving up" Shirou to a bunch of mages), or what they would do with Shirou exactly. But they would obviously study the boy and Kiritusgu. And although they might find some interesting things about the curse, they can do nothing for Shirou's father, who passes away within a month of arriving.

Shirou is obviously effected by his father's passing and blames himself. He learns a lot of interesting things about himself and Clock Tower and is briefly tutored in magic by someone. Because he is without apparent talent, nobody really has much interest in taking him into their house. Clock Tower considers him a closed case and a mage informs him he has less than X years to live. I'm not sure how old Shirou would be at this point. The younger he is, the longer he should be given to live? I suppose it would be interesting if this story focused on a younger Shirou (age 10, 12, or 14?) but I imagine most readers would enjoy an older shirou (16-20+). Clock Tower doesn't have much interest in keeping tabs on him. The curse is considered "non-contagious" and since he has little ability in magecraft, he isn't a threat or an interesting subject. So they practically dump him. Most of his father's assets are taken from him as well. Shirou ultimately return to the town where he was found to seek answers. He isn't one to give up or surrender and probably has a similar level of contempt for mages as his father, perhaps having seen first hand in Clock Tower how they treat others.

4. Shirou's "Hero ideal" burns bright. There's a lot of corruption in Fuyuki City. He comes into contact with Taiga (who was made aware of Shirou when Kiritsugu died?) and goes to live with her, enrolling in school. When he's not attending classes, he's chasing the rumor mill, hunting down mundane serial killers and missing people in the city. He doesn't adopt any kind of persona, but simply wears an (always changing) mask over his face to disguise his identity. He utilizes reinforcement magic, blunted arrows, and sword (it should probably be a mundane one? Perhaps western in origin. He may have received training in clock tower from someone who studies western forms of swordplay?). He continues to try and further his fledgling abilities in projection magic using the pitiful amount of knowledge he acquired in Clock Tower (probably a book or two on projection).

I would envision this part of the story to be about as long as 1+2+3 combined. A whole arc for Shirou fighting crime and getting into trouble. "Mundane" opponents are much more leathal as Shirou has to constantly adapt to his muscles freezing up, reduced stamina and increased fatigue. His wild magic ocassionally does some interesting things and he notices that he has an affinity for projecting weapons, especially swords.

School-wise, he joins the archery club (if he's in junior high, he probabls starts an archery club himself). I'd envision him taking a proactive role unlike in canon, being less passive and trying to further the skills of other people he meets. His "ideals" are a little more mature than canon Shirou in that he sees "saving people" as being something he can do with a sword, but also in more indirect ways, by tutoring them in English (which is he is more skilled at, having lived in Clock Tower for X years), improving their self-confidence, et cetera. This is how he makes an impression on Sakura, who he lifts out of a depression caused by the Matou family's fucked up practices. I imagine he also might meet Rin and the rest of the canon cast from FSN this way.

When Shirou isn't doing these things, he's researching the grail, lingering in the twisted ruins of the fire, and performing crazy experiments upon himself. The curse upon his body is progressing steadily. Things he found easy to do are becoming harder and harder.

I'm now sure how Taiga copes with the fact her young ward appears to be horribly ill, though it might cause her to be less hard on him. Or maybe it energizes her? She might perform more seriously as a teacher and she might take some active role in teaching Shirou swordplay, in a vain attempt to try and build up his strength (it probably does more harm than it does good, since Shirou is exhausting himself from all the things he does every day).

5. Rumors begin to build about a young man who has been directly involved in the closing of several dozen cases over a year. His blood has been found at the scene of several sites and eye witnesses begin to piece together a lopsided description about him.

But ultimately, Shirou is defeated during one of his nightly adventures, barely getting away with his life. He's too sick to fight. The mysterious figure vanishes from the news. It could be his last opponent is a mage or a vampire, to only further show the difference in strength.

At this point of the story is probably where I'd let the person taking on the challenge to maneuver it. There are three, maybe four major parties to consider:

Tohsaka
Matou
Eizenberg
Priests/Kirei

One of them gets directly involved with Shirou. It could be their relationship starts when Shirou encounters them during one of his nightly escapades and it buidls from there, when he's finally worn himself to the bone and defeated. One of them picks him up and restores him. This is the group Shirou is allied with during the upcoming Grail War.

6. The entire point of this story, the entire theme, is supposed to be about "never giving up". I really like how the Fate UBW/Heaven's Feel arcs read. There's a lot of energy because Shirou is really terrible compared to Heroic spirits. He's always being pushed to the limit. He really doesn't stand a chance against someone like Arturia, yet in HF, well, at least in the Sparks Liner High ending, you can really get a lot of satisfaction in how he overcomes the impossible, even if it's at a monumental cost to himself.

The theme of this story is that the fire not only tainted Shirou's body, but that it burned so hot, Shirou only survived, where no others did not, because he used his "self" to protect him. That's my fanon theory for why Shirou is the way that he is; the fire burned away his "soul"; his "sense of self" is completely gone. It's like he has nothing else to live for, but for others. Maybe it sounds a little silly/sappy, but I think it would be fun to write such a crazy character. The whole story is meant to focus around Shirou's will to live - why did he survive the fire when no one else did? Was it simply his blind will to exist? Then, why does he continue to struggle to live, when his sense of self has been burned away?

Anyway, so Shirou is tainted. Will that get resolved? It shouldn't. That's the point of this story. He enters the holy grail war with different relationships and abilities, but he's still ultimately at a massive disadvantage and has to make numerous sacrifices to preserve his crazed ideal. Because he's slowly dying, it also adds an interesting element all the relationships he forms. How would Rin act upon knowing her opponent/"rival"/lover/whatever is practically dead on his feet? How will Sakura cope with the one she admires having little time to live? What does Kirei have to say about Shirou's futile struggle against death?

I think it would be fun if he eventually did overcome the curse upon his body, but it'd have to be for a sequel. The war is over, the grail is gone, and so is his curse. That would leave him no longer handicapped, probably skilled enough to attend Clock Tower if he wishes, or do something else.

Anyway, I'm not sure if this idea appeals to everyone, but I wanted to get it out of my head.

 

What about Avalon? Kiritsugu should have inserted Avalon into Shirou's body. If he did, I'd assume it's not strong enough to fully counter the effects of the corrupted grail curse. Has it prolonged his life?

Also, surely one of those many mages who'd inspected Shirou would've looked closely enough to discover Avalon. Was that one of the things the Clocktower stole from him?

I love the idea by the way.

 

I assumed Avalon wouldn't cure anything, though yeah, that could prolong his life and be the reasonable explanation for it, though if Clock Tower does take it, it would probably result in a rapid deterioration of his body after that, so I'm not sure how Clock Tower would handle that. I assume they wouldn't mind killing Shirou to get the artifact, but it probably depends upon how they can "detect" hidden artifacts, whether Kiritsugu would try to hide it from them/tell Shirou to not let them take it from him, and other factors. It would certainly be interesting and a point of conflict when Shirou goes there.

 

One thing to consider though, that I never truly understood, is that Gilgamesh + Kotomine manages to survives the taint. Perhaps I don't know enough about the story, but what makes Kiritsugu different from Kotomine? Why was one cursed till death, and the other seemingly healthy? It could be an interesting interaction, if Kotomine dangles a "Do you wish to be saved?" in front of Shirou constantly, without ever completely healing him.

As for Clock Tower/Avalon, perhaps we could make them slightly less cruel, and make Shirou trade Avalon for some kind of magic ritual that prolongs the life of his body. Though, the price of this would be that he MUST remain in the Clock Tower to receive treatment. This could be more interesting if Shirou was older when he entered the Clock Tower, but then it'd have to be explained how Kiritsugu lived that long. In any case, losing Avalon allows Shirou to summon another Servant (though probably far less powerful than Arturia), be forced to rely on Kotomine at least once, maybe after some sort of fight.

The final point to be considered is how Dark Sakura with her grail powers would affect a tainted Shirou.

 

Hmm, I think an interesting work around is to say that the Grail has gained Angra Mainyu's sentience. Kiritsugu was negatively effected because he stood in oppoisition to the Grail's machinations. Kirei's true intentions were felt by the Grail when it was destroyed, so it did not negatively effect him. Gilgamesh is a heroic spirit that shared Angra Mainyu's desires, so he was simply reborn from its power.

Shirou is cursed because Angra Mainyu wanted to try and remind the world what had been done to him. His intention was to corrupt Shirou and make him something the world would put their hatred upon, only it didn't work out that way...?

I do like Kirei holding the power of some "cure" over Shirou, however. So maybe there's a better set-up.

=

Another detail I wanted to add is that throughout the story, "cures" are discovered. Rin might find a spell that allows Shirou to dump his "taint" into others, curing himself. Obviously, he'd never agree to it. But I was thinking, it might be an interesting if Rin decided to sacrifice herself, taking up Shirou's taint to save his life. Though that would probably be too melodramatic after a certain point.

Sakura is an interesting dilemma. She could become the vessel for the Grail and perhaps she could purify him upon embracing the corruption within her. Or maybe she wouldn't want to purify him and instead control/empower him? I dunno. Illya could be put a similar situation as well, I think.

=

I hadn't considered what Shirou's relationships or heroic spirit would be during the war. It would be a little interesting if he were forced to fight everyone, so maybe an alliance with Kirei would be the most interesting. It'd be funny if he summoned himself, of course, though I have no idea what Archer would do after evaluating himself.

Short of that, I could see Shirou being given Lancer by Kirei. Or if the person taking up this challenge doesn't mind an OC, maybe they could think of a historical/mythical figure who did much despite having some terminal disease or chronic affliction; they'd be summoned because of Shirou's ties of desperation to the world. He might also get an evil/extra powerful servant because of the grail's cursed energies inside him. Perhaps he's able to summon Angra Mainyu? And that leads to his eventual restoration.

 

Closest I can think of for "chronic affliction" would be Timur the lame, known for having a gimp leg and killing roughly 5% of the worlds population.

 

Magic Johnson.

 

Oh god, Tamerlane as a heroic spirit would be a fun story on its own. Wonder how he would fair against Genghis or Atilla.

 

It did occur to me that Steven Hawking has been enduring the same crippling neurodegenerative disease for fifty years, when the average life expectancy is close to one.

Probably wouldn't work as a story, but it would be rather funny, to have Shirou summon a servant who is so crippled they can't fight.

 

No real life people in fanfiction, ever.

It is a good rule to follow and I haven't seen it fail yet.

 

Interesting rule, but I don't think many people have even attempted to break it that weren't doing a crack fic. I do see some merits with it, of course, but I don't think that's a hard rule that can apply to good authors. Especially when the universe is something "modern", like FSN or HP. Wouldn't it be interesting if someone had an interesting spin on GWB or Obama? Obama actually being a wizard, would be a bemusing detail for a HP story I think, especially if it were set in the current day, with conflicts centered around the US, or something like that.

 

Voldemort conquered Great Britain and is now King of Europe.

Thanks Obama.

 

lol

Also, I think I did find a suitable candidate for Shirou to summon.

http://en.wikipedia.org/wiki/Fisher_King

edit:

Also I think I have some small idea where Natsu was going with the female-Shirou, who had an affinity for Crows and summoned King Arthur...:

http://en.wikipedia.org/wiki/Bran_the_Blessed