"Fate/Apocrypha" is set in an alternate timeline where the Holy Grail War, a ritualistic battle among mages and summoned heroic spirits, diverges from its traditional format. Instead of seven Masters and Servants, the war escalates into a large-scale conflict between two factions: the Red Faction and the Black Faction. The Red Faction, backed by the Mage's Association, consists of seven Masters and Servants, while the Black Faction, representing the Yggdmillennia clan, also fields seven Masters and Servants. The Holy Grail itself is under the control of the Yggdmillennia, who have seceded from the Mage's Association, prompting the conflict.

The story begins with the summoning of Ruler, a unique Servant class designed to oversee the Grail War and ensure its fairness. Ruler, revealed to be Joan of Arc, is impartial and tasked with mediating the war. However, the situation grows more complex as the Red Faction's Servants are revealed to be under the influence of a rogue Master, Shirou Kotomine, who seeks to exploit the Grail for his own purposes. Shirou's goal is to use the Grail to achieve world salvation through destruction, believing humanity's flaws can only be eradicated by starting anew.

The protagonist, Sieg, is a homunculus created by the Yggdmillennia clan to serve as a mana source for their Servants. After being rescued by the Black Faction's Saber of Black, Sieg becomes entangled in the war. He forms a bond with Saber, whose true identity is Siegfried, a legendary dragon-slaying hero. When Siegfried sacrifices himself to save Sieg, the latter inherits his heart and gains the ability to transform into a heroic spirit. Sieg's journey becomes central to the narrative as he grapples with his newfound purpose and the moral complexities of the war.

Key characters include Astolfo, the cheerful and eccentric Rider of Black, who becomes Sieg's ally; Jeanne d'Arc, whose role as Ruler is tested by her growing feelings for Sieg; and Kairi Sisigou, a mercenary mage and Master of the Red Faction's Saber of Red, Mordred. Mordred, the rebellious knight of Arthurian legend, adds a dynamic layer to the Red Faction with her fierce loyalty and desire for recognition. Other notable Servants include Semiramis, the Assassin of Red, and Achilles, the Rider of Red, each contributing to the intricate web of alliances and rivalries.

The narrative builds toward a climactic confrontation as the factions clash over the Grail's fate. Sieg, driven by his desire to protect those he cares about, confronts Shirou Kotomine in a final battle. The resolution of the war hinges on the choices made by Sieg and Jeanne, as they challenge the Grail's destructive potential and Shirou's nihilistic vision. The series explores themes of identity, sacrifice, and the nature of humanity, framed within the high-stakes context of the Holy Grail War.

"Fate/Apocrypha" distinguishes itself from other entries in the Fate series through its large ensemble cast and focus on factional warfare. The story balances action, character development, and philosophical undertones, offering a unique perspective on the Grail War's consequences and the individuals caught in its chaos.