Fate/Prototype is a digest version of Kinoko Nasu's original version of Fate/stay night.

Akihiro is a teenaged boy with fantasies. He's about to have date with his girlfriend Miyuki when he finds a strange carpet on his way home. Home, a pretty and over-energetic girl named Malon appears from the carpet. She tells Akihiro about the world of Phantasia and wants to live with Akihiro. But even if Akihiro loves pretty girls, he becomes angry with Malon's magical powers and drives her away. The maniac wizard, Roll, who wants to kill Malon, doesn't help at all.

Amaumi Haruhiko is a high school student who attends Shimano Academy in a town called Narasakicho. Narasakicho contains an unknown rainbow which constantly overlooks the town and is related to granting a magical wish called "Gift." Gift is a once-in-a-lifetime present between two people. As a child, Haruhiko has been close with his childhood friend, Kirino, until he obtains a new non-blood sister by the name of Riko. Haruhiko develops a strong relationship with Riko until they sadly depart due to the fact Haruhiko's father could no longer support the two of them. After some times passes by, Riko finally returns to the town of Narasakicho, and along with Kirino, starts to attend Shimano Academy with Haruhiko. The series revolves around the relationship among these main protagonists and slowly reveals the story behind both Gift and the rainbow.

Despite the kaleidoscopic magic ingrained in everyday life, Hitomi Tsukishiro's monochrome world is deprived of emotion and feeling. On a night as black and white as any other, amidst the fireworks spreading across the sky, Hitomi's grandmother Kohaku conjures a spell, for which she has been harnessing the moon's light for 60 years, to send Hitomi back in time to the year 2018 when Kohaku was in high school. Hitomi's mission seems unclear, but her grandmother assures her that she will know when she gets there. Following a trip through time aboard a train driven by a strange yellow creature, Hitomi finds herself in stoic artist Yuito Aoi's room, and his drawings flood her world with color. What is Hitomi's purpose there, and why do Yuito's drawings return such breathtaking color to her drab world?