Due to his relationship as a servant, Archer was soaked in black mud and instead of being swallowed, Archer was given a new body. The magic power flowed back to the Master, and the black mud filled Kirei's heart and resurrected him. .

During the duel with Emiya Kiritsugu, they were soaked in the black mud released by the Holy Grail, and saw the conversation between Emiya Kiritsugu and the Holy Grail consciousness. After Kirei Kotomine escaped from the spiritual world of the Holy Grail, he was shot from behind through the heart by Emiya Kiritsugu.

The Fifth Holy Grail War

At the end of the Fourth Holy Grail War, Kirei succeeded his father as the chief priest of the Fuyuki Church. He performed his duties perfectly and was highly praised by the people around him. Became the guardian of Rin who lost his parents; later, he was sent by the church to take over the position of supervisor.

The Kotomine Church is equivalent to a low-level spy who receives orders to recover holy relics. The church is nominally responsible for running the orphanage, but in fact the orphans it takes in become sacrifices to maintain the source of Gilgamesh's magic power.

Before the start of the Fifth Holy Grail War, he used a trick to steal Bazett's Command Seal and became the Master of the Lancer, using his identity as "Supervisor" as a cover. , hiding the fact that he participated in the war and active in secret. His basic policy was to have Cu Chulainn (Lancer) take charge of the reconnaissance and Gilgamesh (Archer) take charge of the final battle. The Command Seal that controls Gilgamesh is on his right wrist, and the Command Seal that was captured from Bazett is on his left wrist.