Kirei Kotomine is the main antagonist of Fate/Stay Night. He was appointed as the supervisor of the fifth Holy Grail War. Kotomine works for the church and is responsible for overseeing the events of the war, dealing with abnormalities in the war, and providing safe haven to Masters who have lost their Servants.
Kotomine is also acquainted with the Tohsaka family and is the guardian for Rin after her father passed away.
Kotomine describes himself as being defective because he is unable to derive joy from things that others see as beautiful, but instead took to things that others see as ugly. His father enrolled him in the church in attempt to introduce the beauty of life to him, and named him Kirei (translates to Beautiful).
Kotomine dedicated his life to the church and trained as an Executor to carry out exorcism missions for the church. Later, he met his wife who took pity to his condition and tried to help him as well. She had a weak constitution and passed away soon after. Kotomine was unable to feel the pain of the loss and lamented his inability to be human.
Later, Kotomine transferred to the Magic Association where he was acquainted with the Rin's father. He took a liking to Kotomine and took him under his wing. Shortly before the fourth Holy Grail War, Kotomine was officiated as a participant. After Rin's father lost his life in the war, Kotomine became Rin's guardian.
Fourth Holy Grail War
In the fourth Holy Grail War, Kotomine and his Servant Gilgamesh and Kiritsugu and his Servant Saber were the last 2 participants of the war. The Holy Grail had almost completely manifested and Kotomine touched it and made a wish for everyone around him to disappear. The Holy Grail granted his wish and caused an enormous fire which consumed everything in the area.
Kiritsugu ordered Saber to destroy the Holy Grail, spilling its tainted contents on to Kotomine and Gilgamesh. Kotomine's heart became tainted and he developed a bond with the source of the taint.
Kotomine then became interested in the nature of the Holy Grail and learned that it was tainted by the Servant Avenger, Angra Mainyu. Kotomine and Gilgamesh decided to obtain the Holy Grail in the following Holy Grail War. Kotomine kidnapped the orphans of the war and imprisoned them in the basement of the church as the source of energy for Gilgamesh.
In the 10 years between the fourth and fifth Holy Grail Wars, Kotomine took Rin under his wing and taught her magic. He was also appointed as the supervisor of the fifth Holy Grail War. Bazett was sent by the Magic Association as a participant of the war but Kotomine killed her and took command of her Servant Lancer.
Kotomine knew that Rin had been officiated as a partipant of the war and pestered her to summon her Servant. After Shirou summoned Saber, Rin brought him to Kotomine to be briefed about the war.
After Shirou was ambushed by Gilgamesh, he inquired Kotomine regarding Saber. He explained that Heroic Spirits shouldn't be able to retain their memory of their participation in previous Holy Grail Wars. He also explained that if Saber obtained the Holy Grail and made her wish, she would die and qualify to become a Heroic Spirit and participate in future Holy Grail Wars.
Shirou was upset that Saber will not be able to attain peace. Kotomine suggested that Saber consume the contents of the Holy Grail to be reincarnated into the world. Shirou also mentioned that Gilgamesh had attacked his home. Kotomine was surprised and promised to investigate him.
Later when Gilgamesh ambushed Shirou and Saber after their date, Shirou consulted Kotomine about it. He discovered that Kotomine was the Master of both Gilgamesh and Lancer. Kotomine kidnapped him and Saber came to his rescue. When Saber reached the church, Kotomine explained the nature of the tainted Holy Grail and the truth behind the fire during the fourth Holy Grail War. He also explained that he didn't lie about not knowing about Gilgamesh, since Gilgamesh acted outside of his orders.
Kotomine ordered Gilgamesh and Lancer to kill Shirou and Saber and left them. Lancer disagreed with Kotomine's actions and decided to allow Shirou and Saber to escape. Lancer was killed by Gilgamesh for his betrayal.
Soon after that, Kotomine and Gilgamesh ambushed Shirou's home. They injured Rin and kidnapped Illyasviel, as she was the vessel of the Holy Grail. They went to the Ryudou Temple to unleash Angra Mainyu. Kotomine could take command over Angra Mainyu and used it to attack Shirou. Shirou projected Saber's Avalon to block Kotomine's attacks and defeated him using Rin's Azoth Dagger.
Unlimited Blade Works
After Rider was killed, Shinji ran to the church to seek safety. Kotomine recognized Shinji's will to continue fighting and allied him with Gilgamesh. After Caster took command of Saber, she ousted Kotomine from the church. He sent Lancer ensure Rin's safety and ally with her and Shirou. He recognized Rin as a potential vessel of the Holy Grail. He then moved to the Einzbern castle.
After Archer brought Rin to the Einzbern castle, Kotomine ordered Lancer to kill Rin. He refused to obey Kotomine's order and Kotomine consumed a Command Spell to order Lancer to kill himself. Lancer managed to hold on and killed Kotomine.
After Caster and Lancer was defeated, Rin sent Shirou to meet with Kotomine. Kotomine explained that there was an anomaly in the war and warned Shirou's about the black shadow. He explained that Lancer was his Servant and requested Shirou's help to investigate the black shadow. Kotomine also explained that Zouken is a monster.
After Shirou and Rin rescued Sakura from Shinji's hands at school, Kotomine treated Sakura. Kotomine discovered that Zouken had implanted his worm familiars into her and turned her into a Holy Grail. He also realized that Sakura had absorbed the spirits of all the defeated Servants up to that point and wanted her to survive to unleash Angra Mainyu. He consumed all his Magic Crest to extract most of the worm parasites from her.
Kotomine explained to Shirou and Rin that Zouken's worm familiars were feeding on her magic energy and it threatened to devour Sakura on Zouken's command. Kotomine trusted Shirou's nature to help Sakura survive to have her complete the Holy Grail within her.
After the black shadow devoured Berserker, Shirou was brought to Kotomine for healing. Archer requested that his arm be transplanted on to Shirou to save him and Kotomine conducted the surgery.
After Zouken had his talk with Shirou, Shirou suspected that Kotomine already knew about the Holy Grail within Sakura and confronted him. Kotomine confessed and explained that the black shadow was Angra Mainyu and it was devouring people for sustenance. Shirou wanted to stop the black shadow explaining that it was a danger to the human race but Kotomine argued that it was yet to be born and was simply acting on its instinct to fulfill its basic needs.
After Sakura kidnapped Illyasviel, Shirou was brought to Kotomine for healing. Kotomine then requested to follow Shirou to rescue Illyasviel, mostly out of spite for Zouken.
Kotomine fought against True Assassin and his Zabaniya was ineffective against Kotomine because his heart was corrupted by Angra Mainyu. Kotomine bound True Assassin and dealt a fatal blow to Zouken using exorcism.
Sakura then confronted Kotomine. He saw through her guise of pretending to be strong and she stopped his heart in response.
In the true ending, Kotomine showed up at the site of the Great Holy Grail to fight against Shirou. Kotomine likened Angra Mainyu to himself and wanted to observe its birth into the world in hopes of understanding himself. He also explained that Shirou was similar but opposite of him in that Shirou desperately tried to seek happiness by helping others.
Kotomine then engaged Shirou in a fist fight. Kotomine's body expired before Shirou was defeated. Kotomine announced Shirou as the winner of the war and passed away.
Kotomine trained as an Executor of the church. He learned exorcism to defeat evil spirits.
Kotomine specializes in performing magical surgeries. He is able to extract Command Spells, extract Zouken's worm familiars, transplant Archer's arm on to Shirou, and perform a variety of healing.
A magic crest is a series of glyphs that are handed down through a magus family. Kotomine consumed his entire crest to extract Zouken's worm familiars from Sakura on the Heaven's Feel route.
Kotomine is proficient in a Chinese martial art called Bajiquan. It is a style which incorporates direct punches with explosive power.
Black Keys are throwing swords used by Executors of the church.
The blade of a Black Key is materialized using magical energy. The blade is only materialized when the key is about to be used, so an Executor may carry several dozen hilts at any one time.
Black Keys are designed to be effective against evil spirits.