A side project of mine at Animesuki. Currently rated T, but depending on how it goes it might change to M.

Disclaimer: I do not own Fate/Stay Night or Assassin's Creed. They belong to their respective owners.

A/N: Those familiar with the source materials would know that neither of them could be called historical accurate, the in-story explanations being that real-life records have been distorted from the truth for various reasons. Similarly, I'm going to take a similar stance regarding any historical 'facts' this story may present so don't bother saying to me that "it's inaccurate!" - its deliberate :D.


The young redhead strapped to the Animus went into convulsions, screaming unintelligible words as overexposure to the machine caused the Bleeding Effect to warp his mind. Only after he was sedated had the researchers managed to gain control of the situation.

"What's going on here, people?" A man entered the room and barked at the technicians. "I only left you for like, what, two days?"

"Sorry Doctor Clarke, but there's been a severe malfunction and we've yet to know what caused it," a trembling technician pointed at the broken machine.

"Malfunction? What were you doing?"

"As per your instructions, 37 hours ago we've strapped the subject into the Animus in order to relive the memory of his ancestor, an Ottoman Sipahi who also secretly supervised Assassin operations in the Middle East during the time of Grandmaster Ezio Auditore da Firenze. But after a few minutes we lost control of the machine; it didn't respond to any of our command and for 21 hours forced the subject to flash-relive the life of his ancestor."

"Twenty-one hours?" Clarke interrogated, noticing the recent signs of chaos. "Then what happened for the next sixteen?"

"W-well, we still haven't figured out exactly how, but apparently the Animus also subjected him to the life of another Assassin, one that we never knew to be related to him. There's no concrete proof yet, but we speculated it to be the memory of Altair ibn al-Ahad."

Clarke fell into silence as he processed those words. They had initially been interested with the boy merely because their research had discovered that one of his ancestors served Ezio Auditore, a prominent Assassin figure of the Renaissance. Had they known that he was also related to Altair, the Assassin Grandmaster during the Crusades whose memory was considered the ultimate prize for the Animus Project, they would have done extra precautions with the boy. Now how the heck was he supposed to salvage this situation?

"I want all videos of activities for the last 38 hours, and all of you must submit a report immediately; heads will roll, I swear it! And get the subject into Secured Room 4 - stabilize him!"

"Doctor Clarke?" A woman called for his name, ignoring the panicking group of researchers.

"What is it, magus? Good news?"

She shook her head before answering. "Bad. Really bad. Let's speak at your office." Both of them then walked away, where the woman broke the news of the Holy Grail War.


Phantom Hero of Justice

Prologue


A man in a lab coat sat in front of his computer as the connection for the video conference was established. "Vidic, we have a problem."

"Again, Clarke?" the man on the other side snarked. "Where was the confidence that managed to persuade the council into expanding the Animus Project on a new location?"

"Shove it, Vidic, this is an emergency," Doctor Clarke hissed, aware that his compatriot still held a grudge over losing monopoly of his pet project. "My team needs to evacuate, fast."

Noticing Clarke's troubled expression, Doctor Warren Vidic decided to humour the man. "Something related to the 'string of unnatural events over Fuyuki City' that you keep reporting, I suppose?"

"Yes. The magus-" Clarke noticed the man of science's eyes flared on hearing the word, "-in our group thought that it's most likely magical in nature, so a few days ago we had allowed her to do some research. Just a few minutes ago she finally got the answer from an insider at the London Clock Tower. It's a secret war between magi."

"What?" Vidic could barely hold his composure. "H-how bad?"

"Terrible. The combatants seem to care little of collateral damage; for a society that's supposed to act in secret they seem to lack subtlety judging by the demolished building and the occasional fireworks. My guess is whatever they're fighting for is judged to be worth the rising the masquerade. Anyway, my team is gonna have to move away until the situation co-"

Doctor Clarke never finished his sentence.

An explosion erupted, followed by a massive conflagration. The building he was in was not an Abstergo stronghold but merely a temporary space, a makeshift lab to hold experiments until their planned base has been constructed; only the Secured Rooms were fireproof. The doctor spent the next few minutes flailing in agony as the flames engulfed him, but his body finally gave up and sunk to the ground, lifeless. Most of his researchers succumbed to the same fate.

Warren Vidic wouldn't know the true nature of the war until several years later.


Emiya Kiritsugu walked the desolate battlefield, wandering without direction. The Holy Grail had been destroyed and the Golden King slain, the many has been saved at the cost of the few. But his body was broken, Kotomine Kirei somehow survived, his wife was dead, his daughter was lost to him, and Fuyuki City was burning. He didn't know what he was exactly looking for but he was desperate to found anything - any spark of hope to salvage the situation.

Screams of agony were heard from a nearby building and Kiritsugu set haste to give whatever aid he could. Most of the structure had collapsed but some rooms were still intact. He encountered some people but they were dying and it was too late to do anything for them. But then he founded a somewhat unscathed room; there was a burned corpse inside but another person was still alive, unconscious even as fire licked his small body. Immediately Kiritsugu put them down and carried him away, stopping only when he had found a safe place, but the boy was dying. With no other options left, the Magus Killer reached for the artifact Avalon and embedded them into the boy, using its miraculous power to save him.

When they boy woke up, Kiritsugu found that he had amnesia; no memories beyond his first name and basic Japanese. The old man decided not to pressure the lad since he seemed to agonize when trying to remember anything else, concluding that he must be traumatized. Poor child, to be a casualty to a war he didn't even know existed…

Now free of the heartless killer's mask he had been donning his entire life, Emiya Kiritsugu decided to make what little amends he could and adopted the boy.


Several Years Later


It was a small and quiet funeral, for Emiya Kiritsugu had few relatives. Aside from his adopted son Shirou, his friend Fujimura Taiga along with her grandfather, and a few neighbours, nobody else attended. Till the end the Einzberns had never allowed him to be reunited with his daughter, punishment for him breaking their deal and destroying the Grail.

Now Emiya Shirou walked aimlessly over Fuyuki City, frustrated and depressed over the sudden feeling of loneliness inside him. For the brief moment of his life Kiritsugu had not only been his father but also his mentor and his idol; even though Emiya Sr. was tormented by his inability to save everyone, Shirou still admired his effort and wanted to be like him. That was why at Kiritsugu's deathbed the young redhead had sworn to follow his father's footsteps and become a Hero of Justice.

But how? Shirou thought. It took him desperate measures to persuade Kiritsugu to teach him even a tiny bit of magecraft since the old man insisted that he had no need to learn such skill, and thought he had managed to sneak into his father's room and copied his secret journal they were incomplete and he could barely understand any of it; Emiya Shirou couldn't speak Magi. At this rate, he would end up as a half-assed magus at best.

When the boy finally took notice of his surroundings he realized just how far had he strayed from the Emiya residence. He could hear distant shouting in front of him, and when he looked for the source he noticed that sound came from a high school.

Homuraba School…hey, that's where Taiga recently got employed…

Curious with all the commotion, Shirou sneaked inside and found that the sound came from the training grounds. It looks like the Track and Field team was doing intense training; he could saw the athletes practicing throwing, running and jumping with great vigor.

There seemed to be a quarrel, with a huge muscled boy rudely pointing his fingers at three other members, spouting degrading insults that the kind boy believed a civilized man should never say to another human being. A large fight almost broke out, but the other members tried to mediate and it seemed all of them were now trying to resolve the situation in their club room, leaving the training equipments unattended.

Young Emiya's eyes became fixated towards the high jump equipment; he didn't know why, but after seeing one of the athletes put all his might during practice the boy suddenly had an urge to try. Perhaps because it was interesting, or maybe he was trying to occupy his mind with something else to drown his sadness, but whatever the reason it may be Emiya Shirou suddenly found himself mustering his strength, preparing to perform a high jump.

"Ergh!" He could've sworn he could felt the tips of his hair touching the pole, but the boy was undeterred. Second try, third…they boy continued the ritual, oblivious to the fact that his little stunt was being observed from afar by two girls. He had performed an impressive twenty jumps when he realized that the Track and Field club had returned and was currently staring at him.

"Errr…ahaha…sorry for intruding?"

"Whelp!" The muscled boy growled. Shirou recognized him as the foul-mouthed person from before. "What do you think you're doing?"

"Calm down, he's just a kid. Let's just-"

"Don't you dare tell me what to do, sissy!" With a menacing face the rude athlete reached for the frightened boy. "I'll teach you to mess with- hrgh!"

It happened in a blur.

Young Emiya didn't understand how, but as he felt fear towards the athlete his eyes moved widely, instinctively looking at all the members to gauge their hostility level while simultaneously searching for viable escape paths. And when the athlete's hand almost reached him, all his mind would register was one thing: Enemy Attacking…Must Neutralize!

Not expecting the little boy to fight back, the muscled bully never saw the assault coming. Shirou's bodies moved without his consent and proceeded to launch a flurry of attacks. The first was a left hand throat punch which collapsed the airway, followed by a right hand attack between the eyes. Next was an arm lock to momentarily disable the arm that was reaching for the boy, followed by a hip throw which sent the athlete to the ground. Not giving the larger boy a chance to retaliate, Shirou then proceeded to embed his knee into his opponent's nether region.

It was the sight of the burly high-schooler writhing in pain on the ground that snapped Shirou from his trance. There was a moment of silence as the spectators tried to register what had just happened. Finally, one the other athlete finally cried "Get Him!"

Eeek! Shirou panicked. And just like that, his body once again moved by itself, his mind giving evasion instructions as angry athletes raged to avenge their uncouth comrade. He might be an asshole but he's their asshole, dammit!

"Why you-!"

"Get back here!"

"Stop running!"

The boy ignored all the shouting, his mind flooded with thoughts on how to escape this mess. His pursuers were faster, but somehow they looked slow in his eyes, and he somehow kept making efficient moves that allowed him to barely dodge every grab attempts while navigating across the school. However, just as he almost reached the gate he realized that something was wrong.

His body was surrendering, and he realized in horror why: it couldn't take it anymore. Back then he was already tired form the jumping and it was the adrenaline rush that gave him much needed boost, but now it almost ran out, so physically demanding were the string of action that had followed. He had never did much exercise before which meant he's not physically prepared for the feats he had just done, and now his mind was giving commands his body cannot follow.

"Got you!" Shirou's train of thought abruptly ended as one of the runners tackled him to the ground. As he tried to stand up Shirou grabbed some sand and threw them at the tackler's eyes which blinded the target, but other athletes soon arrived and now they've completely disabled him. It's over, he's finished. Some hero I am, can't even handle a few thugs…

Just before the athletes could make an example however, an unexpected savior arrived…

"You beasts! What are you trying to do that poor lil' boy?"

"Oh shit…" one of the athletes trembled in fear.

"It's her…"

"Tiger!"

Fujimura Taiga roared at the name pun. "Who are you calling Tiger! And get your hands away from that boy before I eat you limb by limb!"

"But Ti- err, sensei, he was-" the sentence stopped as the dreaded Tora-shinai made its appearance.

"Wait sensei, ain't teachers giving physical punishment ille-"

"Get. Away. From. The boy!"

"Ma'am, yes ma'am!"

"Go home, your club activity for today is dismissed! Tomorrow ALL of you are gonna come to my office, do I make myself clear, ladies?"

"Ma'am, yes ma'am!" The athletes swiftly run away, not willing to earn the ire of the mad woman.

"Now you," Taiga glared at the redhead, "What were you doing here?"

"Ahaha, I was…uh…sightseeing?" Smooth, boy, now she's gonna maul you…

Surprisingly, it wasn't mauling that ensued, but a hug. "You stupid boy…you're not the only one who missed him, you know?"

Shirou noticed that Taiga was crying. "Nee, Shirou. If there's anything wrong, talk to me, okay? Talk to Fuji-nee, Shirou, we're family…"

"I…I'm sorry, Fu- ergh, wha?" Shirou found himself being carried on Taiga's back.

"Err, Fuji-nee, this is kinda embarrassing…" No answer. Oh well, he stayed quiet as he felt guilty for making her worry. He made a mental note to cook Taiga some meal for tomorrow's breakfast as thanks; he may be just an amateur cook, but even now he's certain that he could do better than her.

One thing intrigued him though. Today he did things he never thought he could. His brain knew how to hide, how to run, how to ride, how to…to fight!

Shirou smiled at the realization. Perhaps he can be more than a half-assed hero wannabe afterall…

They boy would later realized that it was this day that he started having those dreams. Dreams of other people's life. Dreams of the shadow warriors. Dreams of his Assassin ancestors.