Makoto Niwa meticulously tallies the amount of positive and negative youthful experiences he engages in as if to grade his own life. When his parents go overseas, he moves to a new town to live with his aunt, welcoming the change and ready for a fresh start. However, as ordinary as he had imagined his adolescence to be, he could never have taken the existence of an enigmatic long-lost cousin into account. Upon moving into his aunt's house, he discovers the cousin he never knew about: Erio Touwa. Despite being Makoto's age, she couldn't be more different: Erio chooses to wrap herself in a futon all day rather than to go to school. She even claims to be an alien, and with a speech pattern and personality to back it up, any chance of Makoto's dreamt-of normal life is instantly tossed out the window. As he meets a string of other eccentric girls in town, Makoto must face the possibility of seeing his youth points in the red. However, he might be surprised by how thrilling an abnormal youth can be.

Deep in the countryside, a man named Okina works as a bamboo cutter in a forest, chopping away at the hollow plants day after day. One day, he discovers a small baby inside a glowing shoot. He immediately takes her home, convinced that she is a princess sent to Earth as a divine blessing from heaven. Okina and his wife Ouna take it upon themselves to raise the infant as their own, watching over her as she quickly grows into an energetic young girl. Given the name Kaguya, she fits right in with the village she has come to call home, going on adventures with the other children and enjoying what youth has to offer. But when Okina finds a large fortune of gold and treasure in the forest, Kaguya's life is completely changed. Believing this to be yet another gift from heaven, he takes it upon himself to turn his daughter into a real princess using the wealth he has just obtained, relocating the family to a mansion in the capital. As she leaves her friends behind to enter into an unwanted life of royalty, Kaguya's origins and purpose slowly come to light.

In Fuyuki City, the Fifth Holy Grail War is about to commence a lengthy battle of blood, death, and misery. High school student Rin Toosaka has trained her entire life for this moment—to become a magus capable of being a Master in the war. Summoning her Servant known as Archer, Rin finally sets foot into the battle. Discovering that one of her acquaintances, Shirou Emiya, is drawn into the war as well, Rin offers to form an alliance for the time being. And as the two of them grow closer, Rin begins to learn more about Shirou's fate and ideals. Nevertheless, her goal remains the same: to win the all-powerful relic that can fulfill the wishes of those who are victorious after the war—the Holy Grail.

Kimihiro Watanuki can see spirits and other assorted supernatural creatures, which is quite a bothersome ability he strongly dislikes. On the way home one day, while plagued by some spirits, he is inexplicably compelled to enter a strange house. There, he encounters Yuuko, a mysterious woman who claims to be able to rid him of the ability to see and attract the troublesome creatures—for a price. She demands that he work at her store that grants wishes to people, and thus begins Watanuki's adventures through weird and wonderful events.