The story of Fate/hollow ataraxia takes place six months after the events of Fate/stay night. Like its predecessor, it is set in Fuyuki City. Bazett Fraga McRemitz, a member of the Mages' Association and a Master in the 5th Holy Grail War, wakes up on the fourth day of the 5th Holy Grail War with a new Servant named Avenger and no recollection of what happened to her before. She and Avenger set out to fight and win the Holy Grail War.
Meanwhile, Shirou Emiya enjoys a peaceful life alongside all his friends from the 5th Holy Grail War. After one of her experiments distorts time and space, Rin Tohsaka leaves for the Mages' Association in England to resolve the issue. The Servants sense a new threat, and dark creatures begin appearing soon after. As a precaution, Shirou goes to ensure no one is in danger, but instead repeatedly encounters a mysterious girl, Caren Ortensia.
Both Bazett and Shirou find themselves trapped in a time loop that lasts four days, starting on the fourth day of the 5th Holy Grail War. Each time they die or survive the four days, they always wake up on the first day of the loop, aware of everything that has happened to them since the first loop began. Determined to break the cycle, Bazett, Avenger, and Shirou fight to uncover the truth behind the endless four days.