In the year 2062, Earth finds itself fiercely battling Artemis—an AI which rebelled against humankind following a grand-scale workforce automation project failure years prior. In the hope of winning the war, a group of three highly skilled human warriors is assembled, known as the guardians of humanity. Empress, the last surviving guardian, wakes up alone in an empty research facility. Unable to recall anything from the past except a place called Lighthouse No. 8, she begins to search for answers. It is not long before she discovers an impending threat from Artemis—and she is the sole person who can save the world from destruction.

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.

When a life ends, its soul departs to its final resting place known as the Soul Society. However, if a soul is left to wander in the human world for too long, it ends up turning into a corrupted Hollow that feeds on other souls. In such cases, spirits called Soul Reapers are needed to eliminate the Hollows and guide the lost souls to the Soul Society. Ichigo Kurosaki and Rukia Kuchiki are two Soul Reapers who are used to dealing with Hollows that appear in Karakura Town. But when they encounter the hostile Blanks—souls devoid of memories and immune to the soul burial used by Reapers—they are thrown for a loop. Senna, a fellow Reaper that neither Ichigo or Rukia are familiar with, comes to their rescue and manages to fend off the Blanks. The mystery deepens when a mirage of the human world suddenly appears over Soul Society. What could be the reason behind the strange phenomena, and how is it connected to Senna, who avoids any questions about her identity?

Having escaped the many horrors of her village, Saya Kisaragi vows to hunt down the monster responsible and make him pay with his life. As she tears through flesh and bone for her vendetta, she encounters SIRRUT, a group of ingenious hackers, who enlist Saya to help them defeat a common enemy—someone she knows all too well. Unfortunately, the path she follows is paved with tragedy, as once again, Saya faces betrayal at the hands of those she has come to trust. With her back against the wall, the fearsome monster slayer must fight with all her strength and skill if she is to overcome this final mission and exact vengeance.