Kirei discovers Risei's body and informs Tokiomi. Kirei is saddened by his father's death, although Archer suggests that his sadness is due to not having had the chance to kill his father himself. Maiya informs Iri and Saber that Tokiomi wishes to form an alliance with them, and Iri agrees to go to the church to discuss the offer. Before the meeting, Tokiomi visits his wife and Rin, giving his daughter a magus book and some wisdom before leaving. During the meeting, Tokiomi suggests a temporary alliance to defeat the other Masters first and ensure that a representative of the three families, not an outsider, will attain the Grail. Iri agrees, but on the condition that Kirei leaves the city and is no longer involved in the War. Tokiomi complies. As they depart, Iri reveals to Maiya that she is the embodiment of the Holy Grail in human form and will soon die to create the Grail near the end of the war. Maiya promises to protect her until that time comes. Meanwhile, Kirei reveals to Archer that his father's dying act was to leave Kirei the remaining Command Seals, restoring Kirei's ability to contract with a Servant. He also tells him the secret reason behind the war: the Holy Grail can be activated only through the sacrifice of seven Heroic Spirits. Thus, even a victorious Servant must die at the end, which is why Tokiomi is reluctant to use his Command Spells, as he needs at least one to force Archer to commit suicide. Furthermore, Kirei still wants to explore his dark desires, and Archer yearns for a more stimulating master. Later, Kirei meets with Tokiomi, who entrusts him with the guardianship of Rin should anything happen to him, and an Azoth dagger as a symbol of his completed apprenticeship. Kirei stabs Tokiomi in the back with the dagger, saying even his own father and master never really understood him. With Tokiomi dead, Archer and Kirei form a new contract as Master and Servant.

After leaving the island, Kiritsugu began living with Natalia, who trained him to become a mercenary like her and travel around the world as a hired gun. Due to his unique magic, Natalia removes several of Kiritsugu's ribs and uses them to create sixty-six magic bullets that have a devastating effect against magi. Natalia and Kiritsugu are assigned to kill Odd Dvorak, a Dead Apostle mage who controls bee familiars that turn their victims into Ghouls. While Natalia boards the plane that Dvorak is taking from Paris, Kiritsugu heads to his destination of New York to kill the mage's associate there. Both Natalia and Kiritsugu successfully eliminate their targets. However, Dvorak was concealing bees in his body which turn all the passengers and crew into ghouls. Natalia manages to get into the cockpit safely, but with the plane filled with ghouls, she asks Kiritsugu to do something for her. He surprises Natalia by saying he already has something planned. As her plane draws closer to New York, Natalia and Kiritsugu talk via radio, reminiscing about the time they spent together and the bond they shared. When her plane is in view, Kiritsugu does what he believes will save more people: to prevent a Ghoul infestation, he blows up the plane with a Stinger, killing all the Ghouls on board and Natalia along with them. Before he pulls the trigger, he tells her he was glad to have her as his mother. As the plane explodes, Natalia is seen smiling. Kiritsugu collapses in grief over losing another loved one.