After a mysterious pair attack Rukia Kuchiki and erase her memories while she is in Seireitei, Ichigo Kurosaki, a substitute Soul Reaper, briefly forgets Rukia, until he is reminded of her by Kon, an Underpod Mod-Soul. Confused, he seeks his town's candy-shop owner, Kisuke Urahara, who opens the pathway to Seireitei for them. Ichigo is then shocked to find that his allies in Seireitei, the Shinigami of the Soul Society, have forgotten him.

Filled with action, Kimi no Na wo Yobu follows Ichigo and Kon as they fight against their former comrades while searching for the missing Rukia and discovering her assailants before they strike again.