Okay, first things first. This is Shirou roughly half a year since the conclusion of the Fate route in the Grail War. He's become more proficient with his magecraft and has studied swordsmanship under Fuji-nee after realizing how vulnerable and weak he was during the war, but he's by no means a master swordsman or even a decent magus at this point. Reinforcement and Projection are still the only things he can do.
As for the crossover itself, I went with the tried and true "It was always there you just didn't see it" method. The IS were developed in the nasuverse but they were based entirely off technology and not magic, so none of the mages in the Grail War cared about them. In other words the two time lines were congruous but unaffected by each other.
Shirou's age is never specifically defined in Fate/Stay Night, partly because that would make him underage for the porn in the game and partly because nobody actually knows his real age. I arbitrarily decided he was 16 during the Grail War since he was a second-grade high school student which makes him 17 at the start of this crossover.
And lastly, I tied Shirou's life into the story in ways that don't really conflict with Nasu cannon. After all, Shirou lived in Japan his whole life, so it wouldn't be strange to have met and interacted with girls who also lived in Japan. It marginally conflicts with IS canon but not in terrible ways.
I sighed to myself when another clueless middle school kid wandered up to me. "You want the high school entrance exams, right?" I asked, already knowing the answer. The kid looked a little sheepish as he answered me. "This big building is really confusing. I don't know where anything is supposed to be..." He trailed off, looking around for some sort of sign to guide him. I gave him my best smile and said, "Don't worry. I'm here to help."
After guiding the lost boy to his room, I wandered the halls in search of other students. When my friend begged me to take his shift guiding people to their high school entrance exams I figured I'd just be standing at the entrance, pointing people the right way. What a joke! This place was massive and confusing and I still don't know how many entrances there are. I finally chose to just start roaming the hallways looking for people myself. There was no shortage of lost looking kids but at least I had a rough idea of the layout by now, so it only took me a few minutes to guide each one.
"Wait!" I yelled, running up to a bewildered young man. "That room you're about to go in- can't you see the 'do not enter' sign? What are you doing?" The boy had an athletic build but was obviously still in middle school, currently sporting a confused expression. "Ah, sorry. I got completely lost and just started opening doors. My name is Orimura Ichika. I'm trying to find room... 106?" His voice tilted up at the end, like he wasn't quite sure himself. Oh, good. That's on the other side of the building and his exam is scheduled to start soon, but we have just enough time to get him there.
"My name is Emiya Shirou," I responded, "and helping people is what I do. Let's get you to your exam." I smiled as the door shut and we started on our way. After all, there was an IS in that room. Who knows how much trouble the kid could have gotten in if he went in there? Luckily I saved him from that, and brought him to his exam room right on time, so he could continue his peaceful and ordinary life in a normal high school.
A few hours later all the exams had finished, leaving me without a reason to continue being here. My friend only asked me to cover his shift today, so tomorrow he'd be back and I'd be home in Fuyuki City. Still... that IS unit had just been sitting there. Nobody was around. It would be fine just to satisfy my curiosity and see it, right? I've never actually seen one in person before, and unlike most mages I actually worked with technology. If you consider broken old appliances to be technology, that is. If no one was around I'd just sneak a peek at it.
Having decided that, I casually meandered over to the room, with its big 'do not enter' sign, and non-suspiciously checked to make sure nobody was around. Satisfied that I wasn't about to get jumped by some imaginary security force I sidled my way inside and quickly closed the door behind me. There wasn't any real light to see by but I could vaguely make out the shape of the IS further into the room, so I blindly made my way there. Well, if I can't see it with my eyes, I'll see it with my magic. "Trace, on." I intoned, starting my aria. Closing my eyes in concentration I focused my will on one of the few techniques I possess; Structural Analysis. I instantly understood everything about this weapon- and make no mistake, it is a weapon- from what materials it was made out of to how it was forged, its history and characteristics, everything.
Now that I knew how it was made, I could Project a copy of it myself. If I wanted to die, of course. The amount of energy in the core was comparable to a divine sword like Excalibur, and even though the two energies were different in nature they would both burn out my magic circuits and leave me crippled, if not dead, were I to recreate them. If I managed to open up more of my circuits it would be a different story, but even with the instructions Tohsaka gives me on occasion it's still slow going.
My musing was interrupted by the sound of people yelling. "Oh my God- that IS is reacting to him! A man!" Snapping out of my thoughts I realized that I had started up the IS without intending to, and there were now three women in the same room as me, gasping and pointing at the sight. Well, damn. I can't say "Don't worry I just used magecraft to instantly understand how this weapon functions" or anything like that, and men can't use IS normally... this is bad. Okay Shirou, you're not the brightest magus in the world, but you can at least talk your way out of this situation, right?
It goes without saying that I soon found myself enrolled in the IS academy as the only male pilot in the world. Luckily no one had attributed my miraculous ability to magic so I probably wouldn't be assassinated any time soon, at least not by the Enforcers. The only other people who know I'm a magus are Ilya and Tohsaka, and they won't be telling the Magic Association about me. I hope. They were both rather angry that I done something so stupid and they became furious when I announced I had to board at the school instead of commuting from home... but I'm sure they won't get me killed. Probably.
As I navigated the super modern school I could feel the stares of hundreds of girls on me. Well, I expected this. In a school with only one guy I'd stand out quite a bit whether I wanted to or not. Trudging along I made it to my first class without any sort of incident, something I was rather surprised about given the number of people not-so-subtly stalking me around. As the homeroom teacher began her introductions I felt a little bit more embarrassed. This was supposed to be a freshman class, and as such my classmates were all two years younger than me in addition to all being girls, though the former reason embarrassed me much more. I was able to take the math and history and such classes with students my own grade, but in all matters IS I truly was an amateur. I couldn't hope to compete with the third-years in operating the machine, meaning I was stuck taking the freshman class. I only hoped that didn't mean I'd be stuck here two years after graduation...
"Emiya-kun. Emiya-kun!" A voice startled me out of my thoughts. Looking up I saw the teacher, Yamada-sensei, leaning over her desk trying to get my attention. "I'm so sorry Emiya-kun, but it's time for you to introduce yourself..." I didn't know why she was apologizing. It was my fault for spacing out during the introductions of my classmates after all, which was not something I'd normally do. I just had a lot on my mind right now. Standing up, I felt the harsh glares of all the girls in the class as the anomaly in their midst prepared to identify himself.
"My name is Emiya Shirou. I am... well, I'm probably seventeen. My hobbies are cooking and repairing old equipment. I look forward to studying with you all for a year." I finished, and prepared to take my seat again. "Um... what do you mean, 'probably seventeen'?" the teacher asked, furrowing her brow in confusion. Realizing that probably sounded strange, I explained my circumstances to the class at large.
"When I was about five I was caught up in the Fuyuki City fire. My parents must have died and I forgot everything but my first name, so the doctors had no way short of guessing to determine my age and birthday. So I'm probably seventeen, though I might still be sixteen or even eighteen," I explained. It wasn't exactly a unique story. The Fuyuki City fire was a national tragedy in which hundreds of Japanese citizens lost their lives and many more were injured or left homeless.
"Emiya-kun..." Yamada-sensei started, with tears in her eyes. Tears? Looking around I saw expressions of shock and pity radiating from all my classmates. What I said wasn't really that strange, right? I mean, everyone knows about the fire, so why would they be surprised to meet someone who lived through it? As I opened my mouth to explain that I didn't need any sympathy for something that happened years ago, my reply was instantly cut off by an unseen assailant ramming a fist onto the top of my head. Clutching my head in pain, I lifted my eyes so I could see just who my attacker was.
"Eh... Chifuyu-nee?" I asked, bewildered, as a second fist crashed down upon my already throbbing skull. "When we're at school call me Orimura-sensei," she coldly corrected me. I was surprised to see one of Fuji-nee's kendo friends here at the IS academy, and apparently as my teacher to boot. I still remember a few years ago when Chifuyu-nee would come over to my stand-alone dojo right next to my house and spar with Fuji-nee for hours, demanding a hot meal directly afterward and often staying the night. Come to think of it Fuji-nee did say something about how Chifuyu-nee was a really famous and powerful IS pilot, but I didn't really keep up with stuff like that at the time.
"Everyone!" her clear and authoritative voice rang out, "I will be your homeroom teacher this year. I will thoroughly train you in the use of an IS." Right as she was finished speaking the whole class erupted into cheering, shouting things like "I came here because I admired Chifuyu-sama!" and "I'll die for Onee-sama!" The morose mood that pervaded the entire class just seconds ago completely disappeared. Wow. I guess she really is famous then?
Chifuyu-nee just seemed exasperated by this. "I'm amazed by how many idiots have gathered this year. Or are they only in my class?" she asked herself. In response to this the cheer erupting from my classmates only increased in volume and energy, as if any word she said would be greeted by nothing but unbridled enthusiasm. "Hm... so that means Chifuyu-nee is my homeroom teacher?" I muttered aloud. Taking this as some sort of cue Chifuyu-nee pointed directly at me and demanded "Can't you even make a simple greeting?"
"Eh... Chifuyu-nee, I didn't-" I tried to say, before she slammed my head down onto my desk. "Call me Orimura-sensei," she intoned.
"Yes, Orimura-sensei," I responded. The only response I could make, naturally.
I could hear the class whispering amongst themselves as they tried to determine what kind of relationship the two of us had. She's only my guardian's friend, though after this display it'll be hard to convince everyone of that.
"Quiet, everyone! I'll be teaching you the basics of an IS for the next 6 months. After that it will be practical training for the remaining 6 months. If you understand then answer me. Even if you don't understand answer me anyway!" Faced with such authority the class could only answer "Yes!" in perfect unison. Seeing her like this reminded me of the regal bearing Saber used to... no, stop that. Focus on the present.
I noticed that Yamada-sensei had launched into a discussion of the history of the IS while I was spacing out, a really basic intro just meant to set the mood for the rest of the information she'd no doubt continue with. This was all stuff in the required reading before attending the school so I wasn't too worried about it. The lecture continued right up until the bell signaling the end of homeroom, so I assumed she'd be picking up on new stuff tomorrow. Not that I really wanted to be an IS pilot to begin with.
My goal in life is to be an Ally of Justice, a superhero who devotes his life to saving others. An IS, while powerful, is illegal to use in any situations other than strictly monitored matches or during emergencies. While I could use one to, say, help victims of a landslide I couldn't use one to hunt down a dangerous Dead Apostle and blow it to smithereens- the IS itself would record that I 'killed' someone and I'd be jailed for life. This made my plans for the future quite precarious, since the Japanese government let me know quite firmly that I didn't have a choice in coming to this academy and becoming a pilot. 'The world's first and only male IS pilot' couldn't just travel the world anonymously, slaying evil and righting wrongs without far too many people paying attention. This is the problem that's been weighing me down the most.
While I pondered my fate at my desk, I noticed a girl standing in front of me. She was wearing the student uniform, of course, and with a start I remembered her introduction from just a few hours ago. This was Shinonono Houki, a childhood friend of mine. She's quite a bit shorter than me now, with long black hair tied into a ponytail and deep purple eyes. "Got a moment?" she abruptly asks, then starts walking without waiting for a reply. Sighing, I rose out of my seat and started following her. I haven't seen her for six years or so, but it seems like she recognized me too.
Houki leads me without talking to the roof, and I follow her in silence as well. After we get there I prompt her, "Did you need something?" She continues to avoid my gaze and question, opting instead to look out over the railing. Well, this is weird. "We haven't seen each other in six years, right?" I ask, which gets a startled response from Houki. She still doesn't seem willing to talk so I continue on a bit. "That reminds me, you won the kendo nationals last year, didn't you?"
"Wha- how do you know that?" she exclaims, clearly surprised. It's not that surprising, is it? "I read it in the newspaper," I answered easily, "and Fuji-nee told me about it as well. Her exact words were something like 'that cute Houki-chan you used to play with won the nationals, Shirou! You should learn from her example!'" This was roughly around the time I quit the archery club, after all. Fuji-nee was probably trying to motivate me to return to the club with tales of how my old friend was excelling in her own efforts, but I wasn't interested in competitive sports at all.
Houki started blushing and fidgeting after I mentioned how Fuji-nee was praising her, so I just continued with this one-sided conversation myself. "Oh yeah, I haven't properly greeted you yet, Houki. Even after six years I recognized you instantly. You haven't even changed your hairstyle," I remarked, causing her to turn away and fidget some more.
"You remembered my hairstyle?" she asks, not looking at me. "Of course," I reply, "It's not like I'd forget you. We used to play a lot together, back when Fuji-nee was still out doing kendo."
Before we could talk any further the bell rang, ending the small recess we were using to catch up. Well, we're classmates now, so we'll have plenty of time to catch up later. Having a friendly face in the oppressive all-female class considerably lightened my mood on the way back to the classroom.
After another class of mostly review from the pre-term assignments, the chime for a break sounded again. I felt my body relaxing, realizing that I had unconsciously tensed during the whole class hour as terms I only vaguely recognized were tossed around with reckless abandon by the two teachers. I read the textbook cover to cover several times before coming to the academy, mostly on Tohsaka's assurance that I would need the knowledge to not expose myself as a magus, but I still had trouble following some of the lecture. I just wasn't good at this high-tech stuff in general. Still, I wouldn't do embarrassingly bad, and I didn't particularly want to excel anyway. Maybe if I had a completely mediocre performance people would stop caring about me and I could follow my ideals.
A man can hope.
Having my train of thought interrupted yet again, I turn to face a strikingly blonde girl who has positioned herself next to my desk. "Huh?" I manage to get out, not having heard what she said at all. "Oh my, what a terrible greeting! You should feel honored just to talk to me!" she announced imperiously. I tried to wrap my head around this proclamation and felt myself failing miserably. My train of thought had just crashed at the station and I was having trouble processing just what was going on right now. "Who are you?" I blurted out, my mouth not getting the memo and deciding to carry on without me.
That seemed to be the wrong thing to say. With a heavy thud she slammed her hands down onto my desk, shouting "You don't know me? Cecilia Alcott?" All I could do in this rapidly worsening situation was shake my head. "I'll have you know I'm the representative pilot from England, as well as the valedictorian of the entrance exam!"
Something clicked in my head. "Oh, so you're pretty important then. Did you want something?" Being a representative pilot is an important position, a symbol of the country they represent. If she went out of her way to talk to me then it must be something serious.
I was wrong. Did she just come over here to brag about her position? She somehow reminds me of Gilgamesh, though he at least had the justification of being the king of everything at one point. This girl is just good at a sport. "...and the only elite who managed to defeat her instructor!" she continued, and before I could pay enough attention to stop myself I responded "I defeated an instructor too." I instantly cringed as the girl halted her tirade to squawk out a "huh?" Okay, not the best idea I ever had. Quickly trying to placate her, I explained the situation as humbly as I could. "The instructor looked down on me because I was a man, and I basically got a lucky shot in and clipped her chin. She would have guarded it easily if she wasn't so prejudiced."
Before Cecilia could form a response, the bell for the next class chimed and ended the conversation for us. "We'll be speaking more about this later," she announced, and strolled to her own desk in a huff.
Well, my story was basically true. The instructor didn't seem to like the idea of a male IS pilot and attacked me with full force. After the training Saber gave me during the Grail War, my body instantly reacted like my opponent was a Servant trying to kill me and launched itself into a counter-attack that was meant to force my opponent back to give me some breathing room. It turns out the instructor was really not expecting me to react at all, propelling herself directly into my attack and taking a brutal blow on her chin that instantly knocked her out.
Which really wasn't good for me, seeing as how the match was recorded and I showed a reaction speed far faster than anything I should have been capable of, considering I had never piloted an IS before. Another stupid mistake in a long string of stupid mistakes. Announcing my victory in class hadn't exactly been brilliant either. I sighed to myself. This was going to be a long year.
Trudging along the path from the classroom to the dorms felt like I was marching to my own funeral. Girls were talking excitedly all around me, passing their first day in an academy designed to teach them their dream job. Meanwhile I was feeling the crushing weight of realization that I really had no way around my current predicament. Just how was I planning on becoming an Ally of Justice cooped up and monitored in this futuristic academy?
Strolling through the dorms, I located room 1025 and unlocked it, letting myself in. At least I wouldn't have to share a room with anyone. After all, I was the only guy in this entire school- "Is someone there?" a voice calls out. No, that must have been my imagination. That was way too feminine sounding and "Oh, are you my roommate? I'm sorry for not dressing; I was just taking a shower." Yes, very feminine. Those curves I can make out beneath her towel are very feminine indeed. The young lady in front of me is currently drying off her hair so she hasn't opened her eyes yet. Would I survive if I jumped out the window right now? Yes. If I reinforced my legs I'd probably only break a few bones but I'd better start running for it now.
"My name is Shinonono Houki," she finished, finally looking up at me. Too late. "Shi-Shirou!" Looking down at her own state of dress, she yells "Don't look!" and I hastily turn to face the other way.
"Why are you here?"
A perfectly reasonable question. "This is my room! There must have been some sort of mistake." I didn't know how else to explain a young man and a young woman ending up with the same dorm room, but that thought was chased out of my head as Houki grabbed a heavy wooden sword and started swinging it at me. Not wanting to be beaten senseless I immediately started running out of the room. Dammit, I didn't want to be in this situation either, so don't attack me! I'd leave on my own anyway!
Stumbling out into the corridor I was greeted by a number of girls in casual clothes. Seeing Houki in that sort of state was too stimulating on its own, and the skimpy tank tops and short shorts these girls were wearing did nothing to calm me down. "Oh, this is Emiya-kun's room! That's good to know," one of the girls commented. It wouldn't be my room for long, I thought. It certainly wasn't proper for a young girl her age to be sharing a room with me, and I resolved to go set this problem straight right then and there. I guess I'd ask Chifuyu-nee first, since I was already acquainted with her and that would speed up the explanation.
"There are no available rooms. Stop being selfish," she coldly answered after I had finished my story. "Wha-what?"
"Did you think the school didn't consider this already? It's getting late. Go back to your room."
"But- but surely there's something you can do! Off campus housing or an apartment or-"
"The matter is already settled." Chifuyu-nee destroyed my arguments with that last statement. I could see in her eyes that there was no further appeal, no compromise. As much as I objected to sharing the room with a girl, in the face of such overwhelming authority I had no other option. As I turned on my heels to head back to my now foreboding dorm room, I briefly considered just sleeping outside. I knew such a shameful thing would only bring down the wrath of the administration on me, but it might still be better than sleeping in the same room as a girl.
Nevertheless I found myself outside room 1025 again. Sighing, I knocked on the door. I wasn't about to let a repeat of earlier this evening happen, and resolved to knocking on the door every time I was about to enter. Houki opened the door for me, looking much more presentable in her kendo attire. "Shirou? What are you doing back here?" A frown creased her brow. "So you really are my roommate then?" she asked. "Yes. I asked the school about it and they said there just are no other available rooms, so we don't have a choice. I'm sorry to be a burden on you," I apologized, bowing deeply.
Houki wasn't to blame in this situation, after all. She had every right to a normal school life with a normal female roommate, and only my stupid blunder before had caused me to enroll in this academy. So in a roundabout way this entire thing was my fault, and it felt worse that it was an old friend of mine that had to suffer because of it. "N-no... you don't have to apologize." she started, turning a little red in the cheeks.
I was embarrassed about this too, so I sympathized with her. She coughed, clearing her throat. "We just have to set some ground rules, that's all. Firstly, about shower usage rules. I'll be using it from 7 to 8. You can use it from 8 to 9." I nodded. It was only fair for her to set the rules, and I'd do my best in following them. I wouldn't want to put her out any more than I was already. We continued setting up timetables and other things that would hopefully minimize the amount of embarrassing situations we could be put in, and finally hammered out something that looked like it would work shortly before lights out.
Even with the screen between our two beds, Houki was too close! Just being in the same room as a girl when she was sleeping kept me a nervous wreck throughout most of the night. I must have ended up falling asleep at some point though, which I guess is good news. If it was anyone other than Houki I doubt I'd be sleeping for a week at least, but I might even get used to this in a few days. Not that I wanted to, but this seemed to be yet another problem I had no way of solving. For now.
After a quick breakfast with Houki it was off to class again the next day. When Chifuyu-nee announced that the class would be deciding on a representative for the school-wide tournaments that happened every so often I just started zoning out. Honestly, I didn't care what kind of standing my class had in comparison to the rest of the school, and I didn't know anyone in class well enough to voice an opinion anyway. This was basically just free time for me to go over the notes I had been taking. That suited me just fine. I didn't really get the part about energy something-or-others the teacher had talked about during- "I nominate Emiya-kun!" a voice rang out in the background. Wait, what? "I second that!" another female voice chimed in. No no no, why would you be nominating me? I clearly have the least experience with IS out of everyone here and it's not like I've even fought a real match before.
Before I could shoot down this absurd development Cecilia beat me to it. "I can't acknowledge this! Having a man as our representative would bring us nothing but shame! Do you expect me to put up with this farce for a whole year? In the first place, it's almost a crime forcing me to live in such an unrefined country like Japan! The culture, the food- everything is at such a low level!"
She might have intended to keep going, but there was absolutely no way I was going to let that slide. "Did a British girl just insult my nation's food?" I asked, steel in my voice. The food I had been preparing for years, the food that Sakura and Fuji-nee and Saber had enjoyed, the food I had dedicated good chunks of my life to learning- she was going to stand there and brush it all aside?
"Britain has many delicious dishes! Are you insulting my country?" she shot back. Yes, I was. I glared at her, challenging her to say another word about food. She leveled a hand at me, pointing as pointedly as she could at my chest. "This is a duel!" she declared. "Fine with me. I don't have a usable kitchen nearby, but we can travel back to my house if we need to. If you've got something closer I'm fine with that too." Who did this girl think she was? I'd bet my cooking against almost anyone, and I even had a few dishes I could bet against Sakura with one hundred percent confidence. If she thought I couldn't cook because I was a man she had another thing coming.
"What?" she asked, confusion evident on her face. Did she not expect me to take her up on the challenge? I did state that cooking was one of my hobbies in my introduction so it shouldn't be that surprising. Then again, judging by how highly she regarded herself she might not have been paying attention before. "Like I said, I'm ready for a cooking contest whenever you are. Japan's food against Britain's food. There are even plenty of foreign girls who go to this school who can judge for us so bias won't be an issue. It won't even take-" a fist slammed into the back of my head. "She was talking about an IS duel, idiot," I heard Chifuyu-nee say behind me.
That didn't make any sense. "We were having an argument about food. How would we settle that with an IS match?" I asked, expecting her to concede the point. Looking around the room, however, it was plain to see that most of my classmates seemed bewildered by my response. 'Tha-that's right!" Cecilia finally spoke up again. "This is an IS academy, so it makes sense that we should resolve disputes with an IS!" she declared. Well, okay, that made a bit of sense. "Fine," I replied. I was much less confident and eager for an IS match, but there was no way I could back down now. I'd have to win this fight, too. I knew I was just being hot-headed, but there were some things which I just couldn't overlook and insulting my food was one of them.
"That settles it. The battle will be held next Monday in the third arena," Chifuyu-nee announced. "Emiya, Alcott, make sure you're prepared." Did she look happy for some reason?
A couple things to note. First, Shirou is an unreliable narrator when it comes to girls. The story is told entirely by his perspective so he often misinterprets the actions of those around him. Just to reiterate this is the guy who had Sakura coming over to his house every day for a year to cook and clean for him, and he never even noticed that she was sweet on him. This guy is so dense he sucks up girls in an orbit around him. So when he makes guesses as to why girls are blushing or saying things he doesn't understand, he's probably getting the reason wrong.
Second, a lot of people seemed upset that Shirou knew Chifuyu and Houki from the past so I figured I'd share my reasons for that with you now. The answer is simply that Houki has no reason to be in the story otherwise. She's extremely anti-social, quiet, and would have no reason to interact with Shirou normally. Shirou, for his part, would not seek out her company for any particular reason. Without that prior connection they simply wouldn't be friends.
'But wait!' you cry, 'they are room mates so they'd have to interact!' Well, no. That was the reason I made Chifuyu an acquaintance of Shirou as well. Using my massive brain I put a few details together in the original story:
Ichika is told there are no extra rooms so he has to share with Houki
Three transfer students show up soon after and all get rooms
Chifuyu is the dorm supervisor of the first year students
It's obvious that Chifuyu simply made Houki and Ichika share a room, for a number of reasons I can think of, most obviously to prevent girls from simply pushing Ichika down and having their way with him in an empty room. So if Shirou didn't know Houki or Chifuyu at the beginning of the story, they wouldn't be room mates in the first place. I hope that clears up a few things, though I know there will still be people who say 'that's just lazy!' Which is true, that was the lazy man's way of solving this problem. I am a lazy, lazy man.
Expect a lot of deviation from the IS storyline in future chapters.