Shirou Kotomine

The Servant summoned by the Einzberns in the Third Holy Grail War. His class is Ruler. His true name is Amakusa Shirou Tokisada. He is one of the masterminds in the story, and the true Last Boss. If ever the Third Holy Grail War were made into a Visual Novel, the ending would greatly differ depending on the choice of the Einzberns. Just as said until now, if they chose Avenger, events would follow the official history—that is, the Fate/stay night route, but if they chose Ruler, the story would follow this Apocrypha route.
After incarnating into a physical body in the Third Holy Grail War, he spent the next sixty years investigating all feasible documents and ley lines available and waiting for the day when the next Fuyuki Holy Grail War—that is, the “Fourth” Holy Grail war would occur.
Having already hypothesized the possibility of a Great Holy Grail War—a situation with seven Servants VS seven Servants occurring instead of a normal Holy Grail War, Shirou promptly joined the “Red” Camp as the dual mediator and Master sent by the Holy Church and quickly summoned Semiramis without delay. In such an abnormal situation with seven Servants VS seven Servants and where even the previous Ruler had summoned his own Servant, the Greater Grail automatically summoned the Ruler for this war, Jeanne d'Arc, but Shirou had included even that into his calculations as an event within his expectations.
There was only one thing that Shirou couldn't predict. That was the event of a homunculus without even a name merely trying to fulfill his meager wish.
In truth, the facts concerning Amakusa Shirou Tokisada's birth and life aren't very clear. What's certain is that he attained the position of being the person with the greatest responsibility and authority in the Shimabara Rebellion. Even if that is merely a palanquin—merely window dressing, this young boy was definitely the ringleader of the Shimabara Rebellion, the greatest uprising in the Edo Period.
In this work, he is the biggest and strongest problem child. The next one after him is Rider of “Black.” At first, Semiramis was the mastermind in the initial stages of the plot. However, all the characters including her who had already been released in Complete Material along with the original setting were deemed to have too weak of an impact as a mastermind. The idea of “doing something that would have been impossible in the original game setting” was one of the concepts of Apocrypha (I also came up with the idea of seven Servants VS seven Servants following that line of thought), and then Makai Tenshou1 served as an even further impetus that made me think, “How about bringing out Amakusa Shirou?,” from which everything started.
A young boy and a young girl. Both of their battles were heavily connected to flags. One who never became a saint, and one who did. Their points of commonality and difference were so clear and contrastive that I selected him as the last boss—it would have been fine if my thought process stopped there.
At that point, a demon whispered to me, “…Speaking of which, the name of the protagonist of the original Visual Novel is… and their age is almost the same too…,” and thus Shirou Kotomine was born. Not only readers, but even my friends often retorted, “Really?,” to me. Sorry, sorry. But this coincidence felt so much like destiny…!
His white hair and dark skin is compensation for his magecraft… or not. In truth, there were complex causes; his hair became white as compensation for when he forcefully incarnated and after that his skin changed color because he needed to conceal himself in the Middle East for nearly twenty years in order to search for catalysts for Semiramis. By the way, he received a catalyst for the empress from the Sophia-Ri family the moment it was decided that he would participate in the Great Holy Grail War, but it seems he secured three other catalysts on his own after searching for nearly twenty years as a precaution.
He hates humans, but he deeply loves humanity. In the Shimabara Rebellion, he witnessed just how strongly low, vulgar and cruel humans could become. They can become like this even towards those of the same race as them. If they encountered others who have a different skin color or different culture, just how much further would human cruelty increase?
These thoughts of Shirou hardened even further in the Third Holy Grail War and the Second World War which happened immediately after. In the end, he concluded that humanity could only be saved with the miracle of the Greater Grail—the Third Magic. He attached himself to the Assembly of the Eighth Sacrament and sometimes served as the mediator in some of the subspecies Holy Grail Wars. He had almost no interaction with the other members of the Assembly, and was viewed as a curiosity by his compatriots who wondered, “How long has this guy been here?”
As a Servant, he would be third-rate if he weren't Ruler, just as he himself declares. It is actually quite novel for a Heroic Spirit and his Noble Phantasms to be of so little use, and he would have a very hard time winning a Holy Grail War. But on the other hand, as long as he is of the Ruler class, he can amass overwhelming advantages with the skills “True Name Discernment” and “Divine Judgement.”
He is the mastermind, but is a good and virtuous being. In the first place, it is a matter of argument whether or not Shirou's actions are truly evil. Because you could say that he guided people through a slight shortcut to the place they would eventually reach someday. However, on the other hand, he is unmistakably evil. Because he tried to save not individual people, but only the human race itself.
Having no hobbies or anything he likes, he lived sixty years for the sake of humanity's salvation. Even if his plans were overturned in the end, the instant when he saw the rising sun as he lay on Semiramis' lap—was a moment of supreme bliss for Shirou.

Fate/Apocrypha material: Fate/Apocrypha Encylopedia
Translator's Notes
  1. ^ Famous Japanese novel with several adaptations.