The theft of the Greater Grail from Fuyuki City leads to a splintered timeline in which the Great Holy Grail War is waged on an unprecedented scale.

A disastrous school trip leaves four students stranded on an uninhabited island. Staying alive on a deserted island is easy for Homare, thanks to her survivalist father's training. While the others struggle, she shows them that being isolated may not be as dreadful as they thought.

Aya Asagiri is a middle school girl who has problems both at school with bullying and at home from physical abuse by her brother. While browsing online, a website pops up on her computer featuring a creepy looking person. This person appears to take pity on her, and announces that she has granted Asagiri magical powers.

Seventeen-year-old Mugi Awaya and Hanabi Yasuraoka appear to be the ideal couple. They are both pretty popular, and they seem to suit each other well. However, outsiders don't know of the secret they share. Both Mugi and Hanabi have hopeless crushes on someone else, and they are only dating each other to soothe their loneliness. Mugi is in love with Akane Minagawa, a young teacher who used to be his home tutor. Hanabi is also in love with a teacher, a young man who has been a family friend since she was little. In each other, they find a place where they can grieve for the ones they cannot have, and they share physical intimacy driven by loneliness. Will things stay like this for them forever?