"Fate/Zero" is a prequel to the "Fate/stay night" series, set ten years prior to its events. The story revolves around the Fourth Holy Grail War, a secret conflict in Fuyuki City where seven mages, known as Masters, summon heroic spirits, called Servants, to battle for the Holy Grail, a mythical artifact capable of granting any wish. The Servants are legendary figures from history and myth, each representing one of seven classes: Saber, Archer, Lancer, Rider, Caster, Assassin, and Berserker.

The narrative begins with the Einzbern family, one of the three founding families of the Holy Grail War, hiring Kiritsugu Emiya, a pragmatic and morally ambiguous mage known as the "Mage Killer," to secure victory. Kiritsugu summons Saber, the spirit of King Arthur, as his Servant. Meanwhile, Kirei Kotomine, a conflicted priest with no clear purpose, is drawn into the war by his mentor, Tokiomi Tohsaka, who summons Archer, the arrogant and cunning Gilgamesh. Kirei himself summons Assassin, a group of shadowy figures capable of espionage and infiltration.

Other participants include Waver Velvet, a young and inexperienced mage who summons Rider, the boisterous and charismatic Iskandar (Alexander the Great); Kayneth El-Melloi Archibald, a prideful and powerful mage who summons Lancer, the honorable knight Diarmuid Ua Duibhne; and Ryunosuke Uryu, a deranged serial killer who summons Caster, the twisted Gilles de Rais. The final Master, Kariya Matou, enters the war to save Sakura, a young girl from the Matou family, and summons Berserker, a maddened knight whose identity is tied to Saber.

The war unfolds as alliances form and betrayals occur, with each Master and Servant driven by their own motivations. Kiritsugu's ruthless tactics clash with Saber's ideals of chivalry, while Kirei grapples with his inner emptiness and growing fascination with Kiritsugu. The conflict escalates as Caster and Ryunosuke unleash chaos on the city, forcing the other participants to confront them. The war reaches its climax with the destruction of the Holy Grail, resulting in widespread devastation and the deaths of many key figures. Kiritsugu survives but is left disillusioned, adopting Shirou Emiya, a boy orphaned by the disaster, and setting the stage for the events of "Fate/stay night."

The story explores themes of ambition, morality, and the cost of pursuing one's ideals, with a focus on the complex relationships between Masters and Servants. The characters' motivations and struggles are central to the narrative, creating a morally gray and emotionally charged tale of sacrifice and consequence.