The setting of Fate/Apocrypha is a parallel world to Fate/stay night where the Greater Grail was removed from Fuyuki after the Third Holy Grail War and disappeared for many years. Around the 2000s, around the same time as the Fifth Holy Grail War would have happened, the group that plundered the Grail, Yggdmillennia, openly declares their secession from the Mage's Association and that they are in possession of the Grail. The Association dispatches fifty magi to retrieve it, but all but one are instantly slaughtered by Lancer of Black. The one remaining manages to activate the reserve system of the Greater Grail, allowing for the summoning of fourteen Servants in total.

It is now the time of the Irregulars. In 1945 the world changed. Physicists opened the gates to hell when the bomb fell. Science collapsed and the world became filled with Irregulars; humans who possessed supernatural talents from birth. 17 year old Eiji Hongo has the power to control the God of Swords, Reppu. Together with this friends, they plan to unite West Dragon city.