Kiritsugu saved Emiya Shirō during the aftermath of the Fourth Holy Grail War in Fuyuki City, later becoming the boy's foster father. Prior to this, Kiritsugu had dedicated most of his life to becoming what he called a 'Hero of Justice', a defender of humanity. Kiritsugu was also a magus, although he never made any serious attempts to train the unskilled Shirō in his craft. He dies several years prior to the beginning of Fate/Stay Night.
Kiritsugu was born to Emiya Noritaka, a fifth-generation magus who researched the vampiric Dead Apostles on a remote Pacific island. It is this research that eventually leads to Kiritsugu's childhood friend and love interest, Shaley, being transformed into a vampire, an event that coincides with the arrival of representatives from the Roman Catholic Church and the Mage's Association. The island is razed and its inhabitants massacred in an attempt to wipe out any remaining vampires, or any witnesses of their existence. Kiritsugu is confronted by Natalia Kaminski, an Association mercenary seeking to kill the cause of the vampire outbreak, namely Emiya Noritaka. Kiritsugu in turn confronts his father, who displays indifference when faced with the results of his work, particularly Shaley's transformation. Kiritsugu then shoots Noritaka in the back using Natalie's gun.
Natalie goes on to adopt Kiritsugu as her apprentice, and later as her partner during the course of her work. Their final mission, involving Natalie boarding a plane in order to take out a target, leads to the both the crew and passengers being turned into Dead Apostles. In their final conversation over the radio, Kiritsugu tells her that he views her as his mother, and that he was glad how they were never lonely when together. He then shoots down the plane using a surface-to-air missile, rather than allow it and over 300 Dead Apostles to land.
Dedicating his life to becoming a "Hero of Justice", Kiritsugu's primary goal was the protection of human life, without exception. However, he came to realize that such an ideal was impossible to realise; for every individual life that he saved, there would be another that he would fail to protect. Understanding this, Kiritsugu decided that, rather than strive to save every single individual, he would take the approach of sacrificing the few to save the majority.
Over the years, Kiritsugu became famed as an expert "Magus Killer", a ruthless man capable of dispatching even the most powerful Magi. During this time, he rescued a girl named Maiya Hisau, and trained her as an apprentice and partner. His reputation continued to grow, eventually leading to his being hired by the Einzbern family of Magi, to act as their representative during the 4th Holy Grail War. Kiritsugu agrees, his intention being to wish away the ills of the world using the Grail's power. He meets and falls in love with Irisviel von Einzbern, the latest in a line of Einzbern homunculi. The couple marry, and Irisviel gives birth to their daughter, Illyasviel von Einzbern, eight years prior to the 4th Holy Grail War.
Using funds provided by the Einzbern family, Kiritsugu spends years making preparations for the war. He is provided with Avalon, a Noble Phantasm excavated by the Einzberns from Cornwall in England, and uses it to summon Saber as his Servant. However, the pair prove to be incompatible as partners, with Kiritsugu's ruthless and underhanded tactics going against Saber's code of honour and chivalry. As a result, Kiritsugu chooses to have Irisviel act as a proxy Master, and liaison between him and his Servant. He bases his strategy on having Saber engage enemy Servants directly, while he dispatches their Masters from a range. His arsenal during the War includes a Thompson Contender pistol, a Calico 960 submachine gun, and a Walther WA 2000 sniper rifle with an attached AN/PVS-4 night scope with IR heat vision.
During their first battle, Saber is injured by Lancer, while Kiritsugu tries to snipe the latter's Master from a distance. The plan fails due to interference from other Servants. The Servant-Master relationship deteriorates after a bounty is issued for the rogue Caster, with Kiritsugu planning to pit the other Servants against one another and sending Saber to kill the weakened survivors. Saber expresses disgust at the plan, and is further angered by Kiritsugu's refusal to address her directly. Kiritsugu would later defeat Lancer's Master, Lord Kayneth Archibald El-Melloi, but fail to kill him when Saber literally steps aside and allows Lancer to rescue him. This further strains ties between the two. In contrast, Saber forms a close friendship with his wife, Irisviel.
Caster is eventually defeated, thanks largely to Kiritsugu's tactics and foresight. Saber goes on to engage Lancer in a one-on-one fight, only to watch the Servant die when Kiritsugu blackmails Lord El-Melloi into activating a Command Spell, forcing Lancer to commit suicide. An enraged Saber confronts her Master regarding his seemingly despicable methods, questioning his stated purpose for seeking the Grail. Kiritsugu angrily retorts that Saber's ideals are naive, and that her mentality not only results in needless sacrifice of life, but in fact perpetautes an endless cycle of war.
During the climax of the War, Kotomine Kirei kidnaps the Vessel of the Holy Grail, namely Irisviel. The remaining Servants enagage one another, leaving Kiritsugu and Kirei to finally meet in battle. The pair are evenly matched, with neither able to gain the upper hand. When Rider's death triggers the near-complete manifestation of the Holy Grail, it disgorges a torrent of ichor that engulfs the combatants, effectively ending the fight in a stalemate. Kiritsugu is taken into the world bound within the Grail itself, and confronted by Avenger, the Servant that had corrupted the Grail during the 3rd Holy Grail War. Avenger appears in the form of Irisviel, trying to tempt Kiritsugu into using the Grail's power. However, upon realizing the tainted Grail could only grant his wish through widespread death and destruction, a shattered Kiritsugu rejects it, and tries to strangle his "wife". Avenger retaliates by infecting his being with the ichor of pure evil and corruption contained within the Grail. Kiritsugu is then ejected from the Grail, where he recovers before Kirei. After a brief exchange during which Kirei begs him not to destroy the Grail, Kiritsugu shoots the priest in the heart.
With all other Masters and Servants defeated save Saber and Archer, Kiritsugu effectively ends the 4th Holy Grail War by activating his two remaining Command Spells, forcing Saber to shatter the Holy Grail with Excalibur. Without a corporeal vessel, the malevolent ichor within the Holy Grail is released in a massive deluge, flooding a portion of Fuyuki City and igniting a raging firestorm. Kiritsugu survives, and saves the life of a severely injured Emiya Shirō by implanting the Noble Phantasm Avalon within his body.
With the War's end, Kiritsugu discarded his merciless facade and adopted Shirō, raising the boy as penance for his past sins. Due to the curse inflicted upon him by Avenger, his body steadily deteriorated over the years, rendering him unable to rescue his daughter Ilya from the Einzberns.
Emiya Kiritsugu dies several years prior to the events of Fate/Stay Night, his mind and heart at ease, confident that Shirō would succeed him as a "Hero of Justice" without suffering his own wretched fate.
A skilled magus, Kiritsugu is capable of utilizing common spells and enchantments such as Mystic Eyes. He is talented in the use of the Emiya family's brand of time-altering magic, specifically the spells Double Accel and Triple Stagnate. The former allows him to accelerate all functions and actions of his body, allowing him to move at superhuman speeds, while the latter slows his bodily functions to the point that his heartbeat is undetectable. Both spells function by isolating and modifying his body's flow of time in contrast to the rest of reality. However, prolonged or frequent usage has detrimental effects on Kiritsugu's body.
Kiritsugu's weapon of choice is a custom Thompson Contender pistol, which he uses to fire unique "magic bullets". He originally owned 66 such bullets, each containing ground-up bone from Kiritsugu's own ribs. Upon contact with a mage's body, the bullets send a wave of magical interference through his magical circuit, literally short-circuiting it. This in turn causes the totality of the afflicted's magical energy to flare up and discharge, causing massive nerve damage and burning out his magical circuit. In the rare event that the afflicted survives the ordeal, he is left almost completely paralysed and unable to use magic. The bullets themselves do not require actual contact with the victim, but may also be fired at extensions of their magical energy, such as their defence spells. Since the bullets act by sending interference through magic the only safe way of defending against them is to use physical means with absolutely no use of one's magical powers.
Unlike most magi, Kiritsugu is willing, and at times even prefers, to use non-magical means of combat. As such he has extensive training and experience in the use of modern weaponry, including various pistols, submachine guns, assault rifles, sniper rifles, explosives, and even surface-to-air missile launchers.