Bazett Fraga McRemitz, a member of the Mages' Association and a master in the 5th Holy Grail War, wakes on the fourth day of the 5th Holy Grail war with a new servant, Avenger, and no memory of what happened to her beforehand. She and Avenger set off to fight and win the Holy Grail War. Meanwhile, Shirou Emiya lives a peaceful life with all his friends, from the 5th Holy Grail War. After her experiment alters the event-horizon changes time and space, Rin Tohsaka leaves for the Mages' Association in England to fix things. The Servants sense a new danger while dark creatures appear soon afterward.

Shirou, as a precaution, sets off to ensure nobody is in danger and instead finds himself frequently meeting a mysterious girl, Caren Hortensia.