The protagonist, Ritsuka Fujimaru, is an ordinary recruit who becomes Chaldea's final hope after a catastrophic event wipes out most of the organization's staff. Alongside Mash Kyrielight, a Demi-Servant who wields the powers of a legendary Heroic Spirit, Ritsuka is tasked with traveling back in time to different historical eras where the Singularities have occurred. Using a system known as Rayshifting, they summon powerful Heroic Spirits from myths, legends, and history—known as Servants—to fight and restore order.

Throughout Fate/Grand Order, Ritsuka and Mash journey to key points in history, including the ancient cities of Mesopotamia, the ruins of Camelot, and Renaissance-era Europe, encountering legendary figures such as King Arthur, Gilgamesh, and Jeanne d'Arc. Each Singularity presents its own challenges, political conflicts, and powerful enemies as they battle corrupted versions of historical and mythological figures who threaten to derail history.

As the pair fights to correct these distortions, Fate/Grand Order explores themes of fate, sacrifice, and heroism. With an ever-growing roster of characters and Servants, the series weaves a narrative that blends real-world history with fantasy, combining epic battles and complex moral dilemmas. The story captivates fans of the Fate series with its rich character development, dramatic plot twists, and the overarching question of what it means to be a hero in the face of inevitable destruction.