The movie opens with Mayuri Kurotsuchi, in his laboratory, being attacked by a mysterious scythe wielder, somehow causing him to lose his memories as a Soul Reaper. After his lieutenant, Nemu Kurotsuchi, arrives to find out what the disturbance is, he begins to panic, having no memory of her. In his state of confusion, he inadvertently destroys a control panel, triggering a massive explosion of reiatsu that covers all of Seireitei in a milky-white cocoon-like substance that spawns reiatsu snakes. Kenpachi Zaraki hurries only to witness the disaster and becomes imprisoned in the reiatsu. The explosion destroys Seireitei and induces amnesia in all the Soul Reapers residing there.
Rukia Kuchiki was later attacked by the same scythe wielder. As it hurtles towards her, she feels something inside her vanish: her heart and memories have been stolen. While Ichigo Kurosaki is asleep, he senses danger and wakes up. For a moment Ichigo then forgot about Rukia but Kon helps by revealing another coded letter from Rukia, similar to the one she left before leaving to be executed in Soul Society. Ichigo and Kon visits Kisuke Urahara, only to discover that he too has completely forgotten Rukia. After being informed by Kisuke about the incident in Seireitei, Ichigo suspects a connection and decides to go to Soul Society.
In Soul Society, Rukia finds herself in a small cabin in the 78th district of Rukongai, Inuzuri, where she (along with Renji Abarai) was brought up in her childhood. She then finds two "siblings" beside her, calling her name and welcoming her with joy. When Rukia asks for their names, they reply by saying that she had promised to give them names a long time ago. Both ask for her to give them their names. Rukia tries to remember and does recall having taken care of the siblings in the same cabin, but cannot remember their names. Having forgotten her time and status as a Soul Reaper, she then questions what she had been doing, at which the siblings answer that she had been sleeping for a very long time.
In Seireitei, Ichigo is confronted by a group of Soul Reapers including Shūhei Hisagi, Renji, and Sajin Komamura) who proceed to attack him after seeing him accidentally use his hollow mask. When Ichigo confronts Renji about using his Bankai, Renji has no recollection of ever learning it. When intruding the Kuchiki mansion, Ichigo finds Byakuya Kuchiki staring at the picture of his late wife, Hisana Kuchiki; Byakuya informs Ichigo that Hisana was raised in Inuzuri. Thanking him, Ichigo hurries to Inuzuri, detects Rukia via smell, and finds her at the roof of the cabin looking over at her friends' graves.
Upon seeing Ichigo, Rukia questions his identity, claiming not to know him. A shocked Ichigo replies, "It's me, Ichigo! Don't tell me you don't remember!" Rukia attempts to, but just when her memories would start to return, a severe headache stops her from remembering, and she is taken away by the siblings. In the cabin afterwards, she asks her "sister" if she had been awake, and not sleeping as the siblings claimed, to which they answered that they did not know. Rukia collapses once again right before she remembers something and holds her head, panting in agony, and is taken away by the siblings again. Meanwhile, Renji is approached by Zabimaru, who questions on why he didn't use Bankai, and Renji tries to remember why he would know it.
Ichigo is seen sitting elsewhere, apparently upset. Kon inquires whether he is sad that Rukia has forgotten him, earning an irritated response in a form of a strike. He points out that Ichigo is strongly connected to Rukia, simply by being the only Soul Reaper who still remembers her. He leaves, and Ichigo, still thinking, pulls out Rukia’s letter. He then has a flashback in which Rukia is writing a letter, which she refuses to let him see, claiming it was a "surprise for later."
Just as Ichigo and Kon prepare to set off, Tōshirō Hitsugaya, Ikkaku Madarame and Yumichika Ayasegawa attack him. Hitsugaya is about to deal the final blow when Renji intervenes, arguing that his soul feels that Ichigo is not the enemy. However, upon hearing Ichigo call him Renji(out of habit), he is quickly angered and warns him not to call him by his first name, though in vain. Several Captains enter the fight to battle Ichigo and Renji, but are interrupted by Urahara and Yoruichi Shihōin, who urge Ichigo and Renji to leave to save Rukia while they hold the Captains off.
To find Rukia, they must use a form of kidō which relies on the bond between Ichigo and Rukia. At first Renji is doubtful, but Ichigo is determined to see it succeed. When the technique is activated, a transparent red thread is shown, which connects Ichigo and Rukia, and through it Ichigo is able to locate her.
Talking to Yamamoto and the other Captains, Urahara reveals that during his time as a Soul Reaper Captain he had experimented on a parasitic Hollow with the ability to erase memories through a scythe-like appendage on its tail, and hypothesizes that the two rogue spirits are being influenced by the Hollow, explaining that, since the memories of each person in Soul Society are linked, the loss of Rukia's memories as a Soul Reaper induces the collective amnesia experienced after their attack.
Rukia wakes up to find herself in Mayuri's laboratory with the twin siblings working on something. They claim that they plan to destroy all those who try to take Rukia from them and ask her why she wants to protect the Soul Reapers. Their conversation is interrupted by the arriving Renji and Ichigo on Hihiō Zabimaru through a wall. Rukia finally remembers Renji, and Ichigo urges her to remember more, stating that the Rukia he knows would never lose herself in such a way.
The siblings, disturbed, try to convince Rukia to leave. Rukia, however, instead asks him to repeat his name, at which her memories return and she chokes out the name Ichigo. The sister declares that she will never forgive Ichigo for trying to steal Rukia. She proceeds to wish that she, her brother, and Rukia would become one, and the two merge with her, resulting in a twisted form of Rukia, referred to as "Dark Rukia" in the trailers. Renji deals with any other enemies for Ichigo, leaving him to do whatever necessary for "that woman."
Ichigo is forced to fight Dark Rukia, evading her attacks instead of fighting back. He asks her to remember him, earning a reply that Dark Rukia will erase her memories of him and destroy their bond. Ichigo, however, retorts that as long as he remembers her, their bond can never be broken. Dark Rukia is almost at the point of decapitating Ichigo when she is interrupted by Byakuya's kidō. Byakuya and Renji inform Ichigo that Rukia is turning into a Hollow and must be destroyed.
Ichigo refuses and emphasizes his bond with Rukia, to which Byakuya replies that he may do as he wishes; Byakuya steps out and Dark Rukia breaks the kido. Dark Rukia immediately attacks Ichigo again, but Ichigo states that it is his turn to give her power this time, much as she had done on their first day of meeting. He stabs her with Zangetsu and gives her his power. With this, the Hollow is expelled from her body and Rukia transforms back to a Soul Reaper, collapsing into his waiting arms. He hugs her with one arm, (his other hand holding Zangetsu) protecting her from the explosion caused by the destruction of the machine in Mayuri's lab, as all the other Soul Reapers apparently regain their lost memories.
When Rukia finally comes back to her senses, Ichigo greets her with his signature "Yo", and then she turns to the injured siblings after Ichigo says so. It is revealed that they were killed by the memory-erasing Hollow, which had escaped Urahara and was possessing a Soul Reaper, and fused with it as they died, reappearing in Hueco Mundo. Because of the Hollow, the memory of the siblings was wiped from Rukia. The siblings complain that they have no one else besides Rukia. Rukia consoles them, telling them that they have each other, and she remembered that she named them 'Homura' and 'Shizuku'. The siblings lose consciousness and die after saying "Goodbye, Rukia", leaving a sad Rukia crying out to the heavens.
In the final scene, Rukia is seen on top of a hill reading a letter given to her by the twins. Ichigo enters, and is questioned if he is going home, to which he answers yes. Rukia tells him that he saved her, and Ichigo replies that she saved him first; he suggests that they were connected even before they met and that their bond was based on that connection as well as their memories. He bids her farewell, addressing her as "Soul Reaper," to which she replies with the exact words from their first encounter: "It's not 'Soul Reaper'. It's Rukia Kuchiki."New Characters