While trying to escape, Kakashi was hit by a rock which he didn't notice because of his bandaged eye causing him to fall. Obito pushed Kakashi out of the path of a falling boulder, causing himself to be crushed beneath it instead. Knowing his life was at an end, Obito instructed Rin to implant his left Sharingan into Kakashi's damaged eye. Rin complied, and as soon as the surgery was completed Kakashi used the Sharingan and his Chidori to kill Kakkō. He then returned to Obito to see if there was anything he could do for him, but the place was turning into shambles, forcing Kakashi and Rin to leave him behind. With the help of Minato, they ultimately completed their mission, allowing them to mourn Obito's supposed death.
Soon after the end of the war, when the Nine-Tails attacked Konohagakure, Kakashi and the rest of his peers were barred from participating in the defence of the village by Kurenai's father and other older shinobi