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.

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?

When Iori Kitahara heads off to college, he decides to live at his uncle's dive shop in Izu named Grand Blue. Iori is looking forward to experiencing college life amidst the roar of the waves, the blazing sun, and his cute cousin who lives with him! However, Iori runs into a group of tough guys playing strip rock-paper-scissors, and ends up joining Peek-a-Boo, the college's diving club!

A new school term begins, as does the season of new encounters. As he surveys his class full of couples, Hashiba Jun'ichi's mind is filled with distress as he asks himself, "Why am I still a virgin?!" Having heard from his friends that the easiest way to fulfill his long-standing desire to graduate from the fellowship of virgins is to kowtow to a gal, Jun'ichi does exactly that and asks his classmate Yukana out. And unbelievably, she actually agrees to date him. What will become of Jun'ichi from now on?

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.

An Intelligence Agent is sent to El Principe, on the border with Morocco, to investigate a possible police collaboration with a terrorist cell but finds unexpected love in the least suitable person: a drug baron's sister.

The whole Sanctuary was misled into danger due to the civil war instigated by the Gemini Gold Saint, Saga. Our story begins right after the end of those events... This is a story of the girls protecting Athena. These are the records of love and fierce fights they meet while opposing destiny on their way to maturity...