The battle rages on as Shirou continues to protect Sakura, now consumed by the darkness. He joins forces with Rin to end the Holy Grail War, while Illyasviel, who knows the truth behind it, confronts her fate. Amidst the chaos, Zouken plots to manipulate Sakura for his own desires. The final fight begins.

In a world where time passes at a crawl and the blood of your neighbor runs blue, 17 year old high school student Ayato Kamina goes about his daily life within Tokyo Jupiter oblivious to the world around him, having been educated with the fact that the all civilization but Tokyo has been destroyed. But all that changes when the mysterious civilization "MU" invades his home, raining destruction down from the sky in the form of strange monsters called Dolems. The events that occur next will lead Ayato to the mysterious woman named Reika Mishima, to the truth of their existence, the discovery of what and who he is, and to the powerful angelic robot RahXephon.