Takes place in the Apocrypha Type Moon Universe. Alaya has sensed the presence of not just seven, but 16 Servants. In response, it sends its most loyal dog, Shirou Emiya, down with the ability to summon Servants.
What if Shirou was found by Kirei instead of Kiritsugu during the fire. This is is the story of Shirou Kotomine, executer and king. Shirou x Fem Gilgamesh/Harem.
What if when Ryuunosuke Uryuu went to summon the caster class servant Gilles De Rais, he ends up summoning Shirou Kotomine the (adopted) son of Kirei Kotomine and an accomplished church executor as the Castor class servant of modern times. (AKA not a counter guardian)
The gods have forsaken humanity and decided to eliminate their inferior counterparts. As a last-ditch effort, the holy grail summoned it's most powerful spirits and gifted the rest of its power to a boy named Katsuki-Kotomine Rei.