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110 years before the battle in the Fake Karakura Town, the then-captains gather to welcome the newest captain.
110 years before the battle in Fake Karakura Town, the then lieutenant of the Fifth Division, Sōsuke Aizen, is greeted his fellow Shinigami as he walks towards his captain's quarters. Standing outside the door, he asks the captain if he is ready. Captain Shinji Hirako tells him to come in. Hirako and Aizen disagree over Aizen's unwillingness to dress up for the ceremony they are to attend and the music that Hirako is listening to. The pair go to the First Division's headquarters, where they are greeted by the lieutenant of the Twelfth Division, Hiyori Sarugaki, who kicks Shinji in the face. Seventh Division captain, Love Aikawa, hits her on the head and tells her to apologize. When Hiyori complains, Love explains that somebody has to keep her in line since her captain is not there. Hirako makes faces at her behind Love's back, annoying both Hiyori and Aizen. While waiting for the others to show up, Hirako notices that the Eleventh Division captain has not turned up, and questions why the tenth generation Kenpachi was even made a captain. Love replies that it cannot be helped, as it is customary for the captain of the Eleventh to be a Kenpachi.
When Jūshirō Ukitake, Shunsui Kyōraku, and Lisa Yadōmaru arrive, Ukitake notes that Kirio Hikifune has not shown up. Hirako comments that the Gotei 13 has been going through captains at a high rate lately, with Rōjūrō Ōtoribashi becoming the Third Division captain two years earlier. Shunsui explains that the Gotei 13 is just going through a period of change and that only himself, Ukitake, and Genryūsai Shigekuni Yamamoto have been captains for over one hundred years. Ukitake tells him he forgot Captain Retsu Unohana. Shunsui says it is a peaceful change, with the former Third Division captain retired and Hikifune being promoted, whereas the previous Tenth Division captain had died. Aizen overhears Shunsui discussing this, causing him to ask to what she has been promoted to. Shunsui tells him that she was promoted to the Royal Guard. Captain Kensei Muguruma interrupts, telling them that the new guy has arrived and Yamamoto had told them to line up. Kisuke Urahara enters the room, wearing a captain's haori. Aizen glances at him and agrees with Hirako's statement that he is lazy.
Urahara's promotion ceremony takes place and Kisuke introduces himself to his new Division.
Kisuke apologizes for being late and asks if he may enter the room. Second Division captain, Yoruichi Shihōin, scolds him for his timid attitude and tells him to act like a captain. Captain-Commander Genryūsai Shigekuni Yamamoto pokes him in the back with his staff and tells him to hurry up. Yamamoto explains that seven days previously, Kirio Hikifune had vacated her position as Twelfth Division captain due to her promotion, and that all other captains received notice that elections for a new captain were to begin. One day ago, on Yoruichi's recommendation, Urahara, who was her Third Seat officer, underwent the Captains Proficiency Test in the presence of Yamamoto and three other captains. Yamamoto confirms that Urahara is the new Twelfth Division captain.
Later on, Kisuke introduces himself to his new subordinates. His introduction earns him a slap from his new lieutenant, Hiyori, who refuses to acknowledge him. Already upset with Hikifune's departure, she refuses to accept somebody from the Second Division as her captain, due to his ties with the Onmitsukidō. Her fellow Shinigami tell her she is going to far, but she retorts that she is only saying what they are thinking. When Urahara nervously laughs, she questions why he is not angry that she is bad-mouthing his old division. Kisuke explains that he had decided that he was now a full member of the Twelfth and will act accordingly. Hiyori refuses to accept this and kicks him before rushing outside to nurse her leg.
Later, Kisuke sits outside to clear his head. Hirako tells him that he suspected that Kisuke would have a rough time and reveals that Hiyori looked up to Hikifune as a mother figure, so it will be hard to try and replace her. Urahara admits that he would like to get along with her, but that their relationship will not be the same. Hirako tells Kisuke that he cannot please his subordinates all the time and he should do things the way he wants to. If nobody follows him, then it means that he was not a good enough to be a captain. As Hirako leaves, he asks Aizen how long he is going to watch, tearing away the Kidō he was using to hide. Aizen tells Hirako that he is a really scary person, but Shinji replies that he is the scary one. The following morning, Hiyori becomes angry with Kisuke when she discovers that he has remodeled the captain's office, installing large pieces of equipment to the room. Urahara replies that it is his room now and says that they should try to get to know each other. When Hiyori refuses, punching him in the face, he asks her to accompany him to the Nest of Maggots.
In the 2nd Division's headquarters, a member of the Onmitsukidō reports that Urahara wishes to enter their grounds, claiming to have already received permission from Yoruichi. Though she does not remember granting such permission, Yoruichi tells him to let Kisuke go wherever he wished, despite a protest from Suì-Fēng. When the gates open, Urahara drags the uncooperative Hiyori by the collar of her uniform. It is explained that the Onmitsukidō was originally a separate organization to the Gotei 13, but when the head of the unit becomes a captain as well, the two units become closely linked. Under Yoruichi's leadership, the commanders of each of the five sections of the Onmitsukidō are seated officers in the Second Division. Urahara tells Hiyori that as the Second Division's Third Seat, he was the head of the Detention Unit. The main duty of the Detention Unit was guarding those who had committed crimes in Seireitei. Hiyori notices his use of the "main" and asks what other duties the unit had. Kisuke tells her that the Detention Unit also investigated and detained any Shinigami who was deemed to be a potential threat to other Shinigami, or might impede the duties of their Division. Such people were locked up in an underground facility in the Second Division's grounds, called the Nest of Maggots.
As they descend into the cave, Hiyori asks if people are really locked up in such a place. Urahara replies that it is a horrible affair, but it is not a prison. While the detainees cannot leave, their movements are not restricted. When Kisuke warns her that someone might suddenly attack her, she asks what they have done. Urahara tells her that they have not actually done anything wrong, but have simply been deemed to be dangerous people, according to Seireitei's regulations. Hiyori criticizes this, but is interrupted by Urahara, who asks her if she knew any Shinigami who has withdrawn from the Gotei 13. He explains that if somebody has to leave the Gotei 13 due to personal circumstances, it is called a "leave of absence". If that leave of absence prolongs and it is unlikely the person will come back, it results in "Decommissioning". Actual withdrawal is actually a cover-up for a Shinigami being transferred to the Nest of Maggots. This is all in accordance with the views of the Central 46.
Urahara tells Hiyori that ever since he took command of the Detention Unit, he has been thinking that if the people kept in Special Detention, while dangerous, were given a suitable environment in which to work, they might be able to turn their dangerous potential into a great power. Then, Hiyori is attacked by a detainee and reaches for her sword. Urahara apologizes for not reminding her that she did not bring her Zanpakutō, stating that the Nest of Maggots is a weapons-free zone. As such, all Detention Unit leaders must be capable of subduing any detainee with their bare hands. After fending off the attacker, Urahara shows Hiyori the only detainee that is placed in a cell, who asks him what business he has here. Urahara tells a shackled Mayuri Kurotsuchi that he has come to offer him the opportunity to leave.
Urahara asks Mayuri to help him establish a new organization, while Ukitake tries to persuade Kaien to become his lieutenant.
Hiyori asks who Mayuri is, causing him to say that she is a boy with no manners. This angers Hiyori, who calls him a white goblin. Kurotsuchi congratulates Urahara on his promotion and turns down his offer to leave the Nest of Maggots, stating that he is satisfied with his life here. When Kisuke points out that there is nothing to tinker with in the detention facility, Mayuri asks why he wants to free him. Kisuke reveals that he is thinking of creating an organization within the Twelfth Division called the Research and Development Institute and that he would like Mayuri to be its vice-president. When Mayuri asks if Urahara wants him to work under him, Kisuke replies that if he were to die, the organization would be his to do with as he pleases. Kurotsuchi smiles, saying that Urahara truly is an unpleasant sort of man.
In the grounds of the Kuchiki manor, Byakuya Kuchiki is practicing his Zanjutsu skills when Captain Ginrei Kuchiki arrives. Byakuya asks his grandfather if he will be staying at the mansion. Ginrei states that he is and tells Byakuya to leave his training session, as he has a guest. As he wonders who the visitor is, Yoruichi appears beside him. Byakuya immediately attacks her, calling her a demon cat. Yoruichi says that that is no way to greet somebody who has come to play with him. Byakuya responds that the next head of the Kuchiki house does not need to play. In response, Yoruichi steals his hair tie using Shunpo, and taunts him. Yoruichi says he will never catch her, which incurs Byakuya's wrath. Byakuya uses his own Shunpo to chase after her, which he says is far superior to hers. Ginrei comments that Byakuya would improve greatly if controls his temper.
Elsewhere, Kaien Shiba repeats to Jūshirō Ukitake that he does not wish to be a lieutenant, saying that there are others who deserve to be promoted ahead of him. Disappointed with his reply, Ukitake turns the conversation to the latest genius to graduate from the Shin'ō Academy, saying that he completed the academy course in just one year. While he is the same age as Byakuya, Ukitake tells Kaien that he had a seated officer position reserved for him before he joined the Gotei 13, and that he is now part of the Fifth Division. Aizen applauds the young Gin Ichimaru for killing his division's Third Seat. Gin claims that the dead Shinigami was not worth his time, to which Aizen replies he is glad to hear that.
With souls mysteriously disappearing in Rukongai, the Ninth Division head out to investigate.
101 years before the battle in the Fake Karakura Town, 9 years after Kisuke Urahara became the Twelfth Division captain, three souls choke on a substance spewing from their mouths. Three shadowy figures watch on as the souls die, with one of them stating that ordinary souls cannot "contain the prototype". A second person asks if they should halt the experiments, but the first replies that they shall continue.
In Seireitei, Hirako greets Kisuke as he passes by with Hiyori and Mayuri. When he calls him Hirako-san, Shinji reminds Urahara that he told him to call him Shinji. He then says hello to Mayuri, who reacts hostilely to being called by his given name. As they begin conversation, Hiyori kicks Hirako, annoyed that he did not greet her. While the two bicker, Aizen asks Urahara if he has heard about the strange disappearances in Rukongai, which has been occurring for the past month. Urahara asks if by disappearing, they mean going somewhere else in secret, but Hirako says that is not the case. The missing souls leave behind their clothes. He goes on to repeat Retsu Unohana's explanation that if they had died, they would have turned to Reishi, and their clothes would have disappeared as well. The only thing they can think of is that without dying, the souls are becoming unstable and unable to maintain a Human form and eventually cease to exist. Hirako says that he does not really understand it, and that the Ninth Division is investigating the cause.
As the 9th Division's captain, Kensei Muguruma, his lieutenant, Mashiro Kuna, and four seated officers march through Rukongai. Mashiro questions why they are there. She says that they should wait for the 10 advance guards to report in and that Kensei is being impatient, as a captain should not need to investigate unknown causes. An angered Kensei is restrained by his subordinates, who remind him that she is always like that and try to calm him. Kensei asks her why she came along, and tells her to go home. Mashiro throws a tantrum, demanding Ogahi (a type of food), but Kens, a young boy, falls at Kensei's feet, and it is shown that a Hollow attacked him. Muguruma uses his Shikai to cause the Hollow to explode and asks his officers if they are all right. Seeing the small boy crying, Kensei tells him that he should be happy that he is alive, and to smile. He hauls the boy to his feet and asks him his name. The boy tries to wipe away his tears as he says "Shūhei Hisagi," Kensei tells him that Shūhei is a strong name, and to quit crying. Hisagi reluctantly agrees, still trying to wipe away his tears. When Mashiro reappears, Kensei demands to know where she was during the fight. She cuts him off by saying she found ten shihakushō in the nearby bushes.
Realizing that his subordinates have vanished too, Kensei sets up camp and sends for a researcher to analyze the area.
Kensei realizes that the ten shihakushō belonged to the ten advance guards he sent out and they were not taken off, but rather the wearers have vanished. He orders Shinobu Eishima to inform Central 46 that they have their first Shinigami victims in the case. He tells Izaemon Tōdō that there might be a pathogen causing the souls to break down, and to request a researcher be sent by the 12th Division. Muguruma instructs Heizō Kasaki have the Division send a tent, as they will be camping there tonight, as he intends to prevent any threats from reaching the Seireitei. His Fifth Seat asks what should he do, and Kensei tells him to search the area with him. Muguruma tells the children to go home before the sun sets, and Hisagi notices the number 69 tattooed on Kensei's chest before he leaves.
In a laboratory of the Research and Development Institute, Mayuri and Hiyori argue about who has their ranks in the Twelfth Division and the Institute. Hiyori then yells for Kisuke, demanding that he do something about Kurotsuchi. Urahara tells her about his prototype for a new Gigai that he has developed in a bid to stabilize the souls that have been disappearing. Tōdō arrives at the laboratory, requesting an audience with Urahara. After being updated about the situation, Urahara promises to send someone that evening and instructs Tōdō to return to Muguruma. Kisuke asks Hiyori to go, but she refuses, demanding that someone of lower rank be sent instead, pointing at Akon, who retorts that she is always complaining and should quit if her job is so bad. Hiyori tries to kick him, but he dodges her. Urahara tells Hiyori that she is the only one he can trust with acquiring a sample from the scene.
Tōdō arrives back at the Ninth Division's camp ground, only to be told he is late. He explains that he went to the Twelfth Division's headquarters by himself and asks to switch places with the Fifth Seat, whom he tells to get some sleep. Eishima explains that only one of the seated officers is to rest at a time, with the other three standing guard. Inside the tent, Kensei, Kuna, and Kasaki are resting. Mashiro begins talking in her sleep, annoying her captain. Muguruma hears a noise outside and, along with Kasaki, rushes to investigate. He finds two of the blood-soaked officers lying on the ground, with Tōdō standing nearby. When Tōdō collapses moments later, Kensei tells Kasaki to be ready, as the enemy is still nearby. Muguruma calls for Mashiro, but as he turns his back, Kasaki's neck is cut. Kensei is shrouded in darkness and stabbed through the back. As the darkness recedes, he turns to see his attacker.
An alarm sounds across the Seireitei, as all captains are summoned to the First Division headquarters for an emergency meeting. Upon hearing that the Reiatsu of Kensei and Mashiro have vanished, Urahara rushes into the laboratory and asks a researcher where Hiyori is. When she tells him that Hiyori has already left, Kisuke rushes off, thinking to himself that he should have went himself.
In an emergency meeting, Yamamoto sends several captains and lieutenants to reinforce the Ninth Division.
At an emergency meeting in the First Division barracks, Yamamoto reports that the Reiatsu of Kensei and Mashiro have disappeared, and the reason is unknown. The Captain-Commander says that this is the worst outcome they can imagine. Until the previous day, the matter only concerned Rukongai, but it is now an issue that must be resolved on the pride of the Gotei 13. As Yamamoto says that he will send five captain-class Shinigami to the scene, Urahara arrives at the meeting. He requests to be allowed to go, but the Captain-Commander declines his request. Urahara tries to argue with him, but is stopped by Yoruichi, who tells him not to lose his composure. She states that since he chose Hiyori to go on the mission, his actions are an insult to her.
Yamamoto selects Captains Shinji Hirako, Rōjūrō Ōtoribashi, and Love Aikawa to go to Rukongai, while Yoruichi is to stand-by for separate orders. Captains Kuchiki, Kyōraku, and Ukitake are told to guard Seireitei. Captain Unohana is told to prepare her medical facilities for incoming casualties. Retsu asks if it would not be better if she went to the scene to treat the wounded more quickly, but Yamamoto refuses to allow the head of medical treatment to go into an unknown situation. As a result, he has decided to send somebody else and invites Kidō Captain Tessai Tsukabishi and his lieutenant, Hachigen Ushōda to enter the room. When he asks them to head to the scene, Kyōraku remarks that it is a bad idea to send both the Kidō captain and lieutenant. When Yamamoto asks what he would suggest instead, Shunsui asks for his lieutenant to be sent. Lisa, who had been eavesdropping on the meeting, agrees to go. When Yamamoto says that Shunsui is doing as he pleases, he replies that it is rare for such an event to occur, and he would like to give her some experience. He comments that Lisa is strong, and asks Tessai if he will step aside for her. When Tessai concedes, Yamamoto finalizes the orders. As they leave, Shunsui tells Urahara not to worry, as Hiyori is strong, though not as strong as Lisa. Not worrying and having faith are also duties of being a captain.
In the forests of Rukongai, Hiyori evades attacks from a large shadowy figure. As the figure attacks again, Hirako arrives. He asks her why she has not drawn her sword. Hiyori replies that she could not draw it. When the moon breaks through the clouds, her attacker is revealed to be a Hollowfied Kensei.
The Hollowfied Kensei and Mashiro attack the reinforcements.
Love and Rose arrive to find that Kensei has turned into a Hollow. Rose states that his mask and Reiatsu are just like a Hollow's. As Kensei roars, Hirako tells them to draw their Zanpakutō, otherwise they're as good as dead. Kensei appears behind Love and attacks him, ripping his uniform and leaving him breathing heavily. Aikawa comments that his power is what he would expect from Kensei. Hiyori tries to stop the others from attacking Muguruma, but Hirako tells her that they have to stop him, especially if that really is Kensei. Lisa says that there are plenty of ways to defeat an opponent without killing them, and decides to cut his tendons. As Rose approaches Kensei, he is attacked from above by a Hollowfied Mashiro, who kicks him into the ground. Kuna then attacks Hirako, but is caught by Hachi's Kidō. Hachi turns his attention to Kensei and casts a Bakudō on him too. When he asks what is happening to Kensei and Mashiro, Muguruma breaks out of the Kidō, stunning Hachigen.
Outside a Twelfth Division building, a dark, cloaked figure walks. Tessai tells the figure that making a cloak that completely blocks one's Reiatsu is not an everyday achievement. Urahara reveals his face underneath the cloak, and Tessai asks him if he is planning on rescuing Hiyori. Tessai tells Kisuke that he thought this would happen when he saw Kisuke at the meeting earlier. Tessai reminds him that they spent a lot of time together at Yoruichi's mansion, so he would not have failed to notice such things. When Kisuke asks if he can pass, Tessai says that he will not allow him to go alone. He says he is sensing an unfathomable terror and that they shall go together.
As Shunsui patrols Seireitei, the Shinigami in Rukongai struggle and come under attack from their own "allies".
As Kyōraku walks around Seireitei in the darkness, he comes across two guards, who ask if everything is all right. Shunsui tells them that he was just having trouble sleeping. He spots Aizen and comments that perhaps he was over-thinking it. When one of the guards asks what he means, he dismisses it as nothing and says that Aizen seems to be having similar trouble sleeping. As the guards say good night to Aizen, Kyōraku tells them to get some rest and they say good night to each other. When he returns to the Eighth Division barracks, Shunsui comes across a young Nanao Ise, holding a book. Shunsui remembers her name, and she tells him she is honored because by this. He tells her that he always tries to make note of the young girls' names, and Nanao visits him every month. Nanao says she wanted to read with Lisa again, but Shunsui informs her that Lisa is not there. When she asks why, he says that she is on an important mission, but will be back by dawn.
In Rukongai, Lisa is injured by Kensei. Rose attacks him, saying that Kensei was not the type of person to attack a woman. Hachigen uses Bakudō #99 Kin to restrain Kensei, commenting that he may have overexerted himself. Hirako asks him if he can do something about their condition with Kidō, but Hachi states that without knowing the cause, there is little he can do. When Hiyori starts coughing again, Hirako tells Hachi to heal all of them, starting with her. Hiyori tells Shinji to let her go, as fluid flows from her mouth. Hirako is cut across the chest as a Hollow mask forms on her face. As Lisa and Love rush towards her, they are shrouded in darkness. Hearing noises in the dark, Love calls out to his fellow Shinigami, but is cut down. As the light returns, Hirako recognizes Kaname Tōsen and asks him why he betrayed his captain. Aizen appears and tells his captain that Tōsen has not betrayed anyone, and that he has followed his orders. Sōsuke asks Shinji not to blame Kaname for what he has done.