"Let us tell the story of a certain man. The tale of a man who, more than anyone else, believed in his ideals, and by them was driven into despair." There exists a plane outside of human concepts, and within there is the Throne of Heroes. Here, the records of famous (and infamous) individuals throughout history are kept, to be used as eternal guardians of mankind. The definition of "hero" is broad — even the most ruthless and heartless are the heroes of their own tales. Centuries ago, three families — Einzbern, Makiri, Tohsaka — conducted a dark and bloody ritual; Heaven's Feel, the Holy Grail War of Fuyuki. A battle between seven magi, competing for a chance to wish upon a "Holy Grail", the 726th branded by The Church. Heroic Spirits from the Throne are summoned and bound to the material world, becoming "Servants" to their summoner "Masters". To keep their true names hidden, the seven Servants are sorted into one of seven Classes: Saber, Archer, Lancer, Rider, Caster, Berserker, and Assassin. In addition, each Servant is armed with the mysteries that symbolize their legend — Noble Phantasms, legendary armaments and abilities, the very concepts that embody their fame. As each Servant falls, the Holy Grail receives their power, until only one remains and the Grail is able to manifest in the physical world to grant the winners' wishes.

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. This marks the start of the Great Holy Grail War in Trifas, featuring two different factions, the Black Faction (黒の陣営, Kuro no Jinei), whose members are part of Yggdramillennia, and the Red Faction (赤の陣営, Aka no Jinei), whose members were sent by the Mage's Association with the exception of one from the Church. The Grail itself also summons Ruler to act as a mediator of the Holy Grail War.