The movie opens with Mayuri Kurotsuchi in his laboratory, being attacked by a mysterious scythe. Stumbling, he accidentally hits a control panel, triggering a massive explosion of reiatsu that envelopes the entirety of Seireitei in a cocoon-like substance. Kenpachi Zaraki hurries, only to witness the disaster; the explosion destroys Seireitei and causes amnesia in all shinigami residing there.

Rukia, who was away from Seireitei and therefore safe from this incident, is attacked by the same scythe. As it hurtles towards her, she feels something inside her vanish; Rukia's heart and memories have been stolen. Meanwhile, in the human world, Ichigo senses danger, and he realizes that Rukia's existence had vanished from his mind for a moment. Kon, on the other hand, reveals another coded letter from Rukia, similar to the one she left before leaving to be executed in Soul Society. 

Ichigo and Kon visit Kisuke Urahara's store, only to discover that he, too, has completely forgotten Rukia. However, they do learn from him that a part of Seireitei was destroyed, and there may be a relation. Ichigo remarks Rukia as "a precious comrade", earning a smirk from Urahara, who opens a gate to the Soul Society. 

Meanwhile, 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 who they are, they reply 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 the names. Having forgotten her time and status as a shinigami, she then questions what she had been doing, at which the siblings answer that she had been sleeping for a very long time. 

Ichigo, now in Seireitei, is confronted by many shinigami (including Renji) who proceed to attack him after seeing him accidentally release his Vizard form. When intruding in the Kuchiki mansion, Ichigo finds Byakuya Kuchiki staring at the picture of his late wife, Hisana Kuchiki, who informs him that Hisana was raised in Inuzuri. Thanking him, Ichigo hurries to Inuzuri, detects Rukia by her 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 tries to remember him, 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 the sister if she had been, in fact awake, and not sleeping, as the siblings claimed, at which she earned the answer that they did not know. Rukia collapses once again right before she remembered something and holds her head, panting in agony, and is taken away by the siblings again. 

Ichigo is seen sitting elsewhere, apparently in a bad mood. Kon inquires whether or not 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 shinigami 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.” 

Later, he is seen fighting again, against Tōshirō Hitsugaya, Ikkaku Madarame and Yumichika Ayasegawa. 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 (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. Urahara urges Ichigo and Renji to leave to save Rukia. 

To find Rukia, they must use a kidou, which relies on the bond between Ichigo and Rukia. First Renji is doubtful, but Ichigo is determined that it will 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. 

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 shinigami. Their conversation is interrupted by a wall, broken down by the arriving Renji and Ichigo on Zabimaru in bankai. 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, tries 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 would never forgive Ichigo for trying to steal Rukia from them. She then proceeds to wish that she, her brother, and Rukia will become one, and it is granted, resulting in a twisted form of Rukia (picture above), 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 Rukia, but never attempts to actually attack her, instead only evading her attacks. He desperately asks her to remember, earning a reply that Rukia will erase her memories of him, destroying their bond. Ichigo, however, retorts that as long as he remembers her, the bond can never be broken." Dark Rukia is almost at the point of decapitating Ichigo, when she is interfered by Byakuya's kidō. Byakuya and Renji inform Ichigo that Rukia is turning into a Hollow and must be destroyed. 

Ichigo refuses, emphasizing on his bond with Rukia again, to which Byakuya replies that he may do as he wishes, and breaks the kidō and steps out. Dark Rukia immediately rushes to 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, Rukia transforms back to a shinigami, and immediately collapses to his arms. He hugs her with one arm, as all other shinigami apparently regain their lost memories. 

When Rukia finally comes back to her senses, she brushes Ichigo's hand away from her face. Ichigo greets her, before she turns to the injured siblings. The two siblings complain that they have no one else besides Rukia. Rukia consoles them, telling them that they have each other, and she then names them "Homari" and "Shizuku." The siblings lose conscience and fade from sight, leaving Rukia crying and calling out their names. This scene is more than likely tied to the title of the movie. 

In the final scenes, Rukia is seen on top of a hill, reading at 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, at which Ichigo replies, saying that it was none other than her that saved him first, and 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 a "shinigami", to which she replies: "It's not shinigami. It's Rukia Kuchiki," the very words she had said to him at perhaps the most important moment of the storyline of Bleach, and the marking of its beginning.