"I will give you power to save all of these lives," said Alaya, in a monotone voice.
"Sorry, I don't think I will accept it, I know what would happen to me if I did," replied Shirou Emiya, smiling bitterly, knowing how many lives would be lost because of his decision.
"... What if I were to tell you that I want a different contract, Shirou Emiya."
"Then, for starters, I would want to know the terms of this different contract,"
"I will grant you pseudo-immortality to live so long as humanity exists. You will protect it as long as you live. And, of course, the quality of your magic circuits will be boosted to do your job better."
"So, pseudo-immortality, and I don't have to obey you like a chained dog?"
"Correct."
"Well then, I accept."
"Very well, Shirou Emiya."
A bright light enveloped the surroundings as Shirou Emiya became the first person ever to be in pseudo-service to Alaya.
500 Years Later
Shirou lost count of how old he was, he only knew that he was to protect mankind. And, protect mankind he did, he eventually managed to successfully kill almost all of the Dead Apostle Ancestors who threatened the existence of humanity. He had, after long years of research, put an end to Type-Mercury. He had even managed, with the help of Alaya, slew the various types in the solar system before they could descend on Earth and wreak havoc.
As he walked on some unnamed to planet, he reviewed the information in his head:
Alias: The Great One
Origin: Another universe entirely
Threat Level: EX++
Weaknesses: As of now, none.
Abilities: Limited reality warping
Shirou let out a deep sigh, it seemed that this battle might be the last one he would have.
He trekked forward until he saw it, a formless black spot in the landscape. Just looking at the... thing made his head explode in pain. He was not able to comprehend what it looked like, maybe it didn't have a look? Regardless, the land around him seemed to warp and change form constantly. It was liquid, it was a solid, and it was a gas at the same time. Without hesitation, Shirou raised an arm, and a wall of weaponry appeared that blotted out the sky and fell upon the anomaly in the universe.
Many of the weapons simply turned into some unknown substance that did nothing and the ones that were not affected shattered harmlessly against the creature. Shirou clucked his tongue and started tracing more heavy weapons such as D and C-ranked noble phantasms to attempt to destroy the Great One.
It shifted a little and did something that caused the entire planet to shake and dropped Shirou to the ground with his ears and nose bleeding.
"AAAARRRGHH! Dammit!" screamed Shirou in pain.
He started stepping his attacks, he started throwing conceptual weapons that could hopefully slow down the monstrosity. With little success he decided to resort to his trump card, his ace in the hole.
"I am the bone of my sword,"
The Great One, immediately understanding that something potentially dangerous was happening, started rushing towards Shirou.
"Steel is my body, fire is my blood,"
Over a thousand different chains of differing quality appeared in a blue flash and held down the desperate creature.
"I have created over a thousand blades,"
The Great One broke out of the chains only to be immediately crushed under the behemoth-sized divine weapon, Ig-Alima.
"Unknown to Death, nor known to Life,"
The creature was continuously buried underneath thousands, no, millions of varying weapons even as it vaporized all of them.
"Have withstood pain to create many weapons,"
It once again did something that caused half the planet to convert to the oddest substances, the weapons weighing him down to dissolve, and for Shirou's body to feel as though it were burning from the inside out.
"Yet, those hands will never hold anything,"
The Great One was just before Shirou, allowing him to feel the effects of being to close to it. (slightly melted skin.)
"So as I pray, Unlimited Blade Works."
The entity let out something akin to a roar as the planet was consumed in a bright light, fading to reveal the Reality Marble of Shirou Emiya, Unlimited Blade Works.
"Let's finish this, you blight," muttered Shirou as he picked a random sword from his infinite supply of weapons.
Three days later
The entire planet the two beings had fought on had been disintegrated by the first day and by this time, they had burned through two more. Shirou was quite glad that this being was quite a few light years away from the nearest human colony. He was also tired beyond belief, his left arm was beyond functioning, and his left leg had been converted into an alien substance that hurt Shirou's head whenever he tried to analyze whatever it was with Structural Analysis.
But, it seemed to be the final fight. The Great One was no longer moving and Shirou still had some prana to spare. He traced a nameless, but extremely powerful sword that was a conceptual weapon that was "to be able to cut through anything" and limped towards the downed entity. Suddenly, it sprang up and touched Shirou lightly. The effects of it were nothing but light, however. Shirou was blasted away over a hundred feet with a hole where his stomach used to be.
As he gurgled on his own blood, Shirou used all his remaining prana to trace every single possible conceptual weapon he had that had the capabilities to force the concept of mortality on the Great One.
As it was under barrage from his weapons, Shirou rushed with the nameless blade, noting that conceptual weapons had not disintegrated and had stayed embedded in the featureless form of the Great One. With one final yell, he swung his sword cutting the black spot on the universe into two.
He watched it, relieved, as the two parts gradually disappeared. And, he promptly fell unconscious. Had he not fallen unconscious, he might have noticed that the battle between the two had greatly weakened space around them and if was further destabilized when the Great One's existence ended.
Slowly, a rip in space opened where the Great One died, and without warning, swallowed up Shirou while he was blissfully unaware of the fact.