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.

As Saber chases Rider through the city on her motorcycle, Kiritsugu investigates and concludes that Rider was not responsible for attacking Iri and Maiya. Saber catches up to the real Rider and Waver, and the two Servants duel, resulting in the destruction of Rider's chariot. Meanwhile, concluding that the Matous were behind his wife's kidnapping, Kiritsugu tortures Kariya's brother Byakuya, who reveals that Kariya was working with Kirei. Kirei made a deal with Kariya to kidnap Iri using Berserker's Noble Phantasm, which allows him to disguise himself as another hero (in this case Rider), in return for the restoration the two Command Seals this consumed and the promise of a duel with Tokiomi at the church. When Kariya leaves, Kirei orders Zouken, who has been hiding and watching them, to show himself. Zouken remarks that he and Kirei are the same in their enjoyment of watching Kariya suffer, before he is driven away by Kirei. Kariya arrives at the church to duel Tokiomi only to find his corpse. Aoi arrives at the church soon after, and on seeing the two of them believes that Kariya is her husband's killer. As Aoi weeps for Tokiomi, she angrily asks Kariya if he is happy now. A confused Kariya attempts to explain the situation and places blame on Tokiomi for his treatment of her and Sakura, but Aoi reprimands him, stating that he doesn't understand her and that he's never loved anyone. Kariya snaps and strangles Aoi. By the time he comes to his senses, he has killed her. As Kariya stumbles out of the church in despair, Archer and Kirei are shown to have been watching from the balcony, enjoying the tragedy as it unfolded.