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A plus soul is chased by a hollow in a local park. Ichigo Kurosaki and Rukia Kuchiki appear and dispatch of the hollow and send the soul off to Soul Society. Comically, Ichigo finds his body inspected by medics, having turned into a Soul Reaper without placing an artificial soul within his body. He escapes from the scene with the aid of Rukia. Soon after, unidentified ghost-like spirits begin appearing in Karakura Town. A mysterious Soul Reaper who calls herself Senna appears and begins destroying the spirits. Ichigo and Rukia return to their Soul Reaper forms (Ichigo this time through the use of Kon, a mod soul) then confront her, but she refuses to answer any questions and leaves. In the battle, Kon notices a figure wearing dark armour among the spirits. Ichigo follows Senna while Rukia returns to Soul Society in order to search for answers. Ichigo encounters Tōshirō Hitsugaya and Rangiku Matsumoto while following Senna, who tells him to come with them to the Urahara Shop, having been sent to earth to investigate why the real world is suddenly appearing as a reflection in the sky in Soul Society, having been noticed by Ikkaku Madarame and Tetsuzaemon Iba.

Back at the Urahara shop, Kisuke Urahara explains that a dimension between Soul Society and the real world, the Valley of Screams, has expanded to the point that it is connecting the two worlds. The spirits seen earlier are "Blanks", souls without memories that were lost in the space between the two worlds and that comprise the Valley of Screams. The memories of the Blanks combine to form a single entity, the "Memory Rosary." Deducing through the use of Kon having witnessed the armoured figure from before, he instructs the Soul Reapers assembled to find the Memory Rosary before this mysterious group does. Ichigo once again follows Senna around, where they make a scene at a nearby mall. Shortly afterwards, Senna is attacked by the armoured beings, and Ichigo arrives to fend them off, not knowing their motives.

While trying to help a soul find his father, Senna and Ichigo travel to a monastery, when suddenly officers from the Gotei 13, namely Renji Abarai, Jushiro Ukitake, Soi Fon, Toshiro Hitsugaya and Rukia appear at the monastery along with some armed forces. They declare that Senna is the Memory Rosary, and order Ichigo to hand her over, but Ichigo, valuing her as a being and not an object, refuses. The mysterious group arrive, calling themselves the "Dark Ones", and are identified as a group of exiles from the Soul Society seeking revenge for the past, appearing and capturing Senna while managing to fight off the Soul Reapers and Ichigo. In the ensuing battle, Ichigo is mortally wounded and is taken back to Urahara Shop, where Orihime Inoue proceeds to heal him. The Dark Ones take Senna to the Valley of Screams and attach her to a device powered by the Blanks that will cause the Valley to collapse, resulting in a collision between the real world and the Soul Society that would destroy both worlds.

Ichigo travels to the Valley to rescue Senna while Rukia goes to get reinforcements from Soul Society. However, Captain-Commander Shigekuni Yamamoto-Genryūsai wants to destroy the Valley before it collapses and refuses to order a rescue mission with only an hour left. In the Valley, Ichigo is overpowered by the large number of blanks and by the Dark Ones, but he is saved by the arrival of his Soul Reaper counterparts, Soi Fon, Izuru Kira, Renji, Byakuya Kuchiki, Toshiro Hitsugaya, Rangiku Matsumoto, Kenpachi Zaraki, Yachiru Kusajishi, Ikkaku and Yumichika Ayasegawa. In the meantime, Jushiro Ukitake convines the Captain-Commander to prolong the destruction of the Valley so that the Soul Reaper force in there may complete the mission and escape the Valley beforehand. The Soul Reapers quickly defeat the Dark Ones and Blanks, and Ichigo battles and eventually defeats their leader, Ganryu. The Soul Reaper force then quickly leave the Valley and reappear in the real world, content in finishing the mission.

However, the process of the collapse has gone too far to be completely stopped. Senna sacrifices herself to push the two worlds back apart to save Ichigo, using the power of the blanks to trigger explosions between the Real World and Soul Society in order to stabilise both. Afterwards, when both worlds have been saved, Senna, weakened by her efforts to restore the worlds asks Ichigo to take her to the graveyard so she can see her name on her gravestone. Though the stone is blank, Ichigo lies and tells her that her name is on it. Believing him, she expresses contentment that she once had a life of her own before fading away. Rukia notes that once the power of the Blanks fades away, so will all memories of Senna. However, the last scene shows Ichigo walking on the bridge where the portal to the Valley was and sees a red ribbon, the one that he had bought Senna, floating down from the sky, and sees a girl who looks just like her running past him, causing him to smile.