This is a story of connecting shining emotions. Joy, sadness, anger. Feelings are a power, invisible to the eye, that every person possesses. Sometimes this power is even capable of changing the world. Hiori Hirahara always has a positive attitude and can't leave people in trouble alone. Ruki Hanari is socially awkward, she wants to get along well with others, but she doesn't know how to go about it. How will the meeting of these two wildly different girls change not only them, but the world itself?

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.