He lost both of his biological parents to an accident and whilst trapped beneath the scrap and debris, he was saved by Kiritsugu Emiya who later became his adoptive father and mentor.
He followed Kiritsugu to Fuyuki City, to investigate the Sakatsuki family. When they arrived, the city was engulfed by a black shadow. Shirou noticed a pillar of light in the Sakatsuki estate and saved the Child of God from a collapsing roof. Through some unknown means, she was born as the perfect vessel of the Holy Grail.