After dealing with Evangeline, Negi takes the class on a trip to Kyoto while searching for more information on his father's whereabouts but is forced to fight against Eastern mages aiming to kidnap Konoka with the help of other students who also become his partners including Nodoka Miyazaki, Konoka's childhood friend Setsuna Sakurazaki, and lastly with Konoka herself. The arc also introduces Fate Averruncus, another mage who looks to be around Negi's age but proves himself to be far stronger than him. Seeing his own weakness after the events in Kyoto, Negi begins to train with several students in order to become stronger while Kotaro Inugami, one of the foes he confronted there unexpectedly reappears and finds himself a family with Negi's students Natsumi and Chizuru. Kotaro also joins Negi against Wilheim, an old evil from the past who like Fate Averruncus, seems to be a pawn of an even stronger enemy.