Ichigo, Chad, Orihime, Uryū, and Yoruichi arrive in Soul Society, but are stopped from entering the gate of the Shinigami citadel Seireitei by Shinigami captain Gin Ichimaru, and must seek another entrance. Yoruichi takes the group to the home of her old friend Kūkaku Shiba, who owns a giant cannon usually used for fireworks, but is capable of launching other objects else where. Kūkaku agrees to fire them into Seireitei, and sends an assistant with their group, her brother Ganju Shiba, who has hated the Shinigami organization ever since his Shinigami elder brother Kaien Shiba was killed by another Shinigami during a mission. The cannon is a partial success and the party lands in Seireitei, albeit with its members split up.
Meanwhile, the flashy entrance attracts the attention of the highest Shinigami military command, which issues orders mandating the immediate capture of the intruders. Ichigo and company all continue to advance through Seireitei regardless, making short work of the rank-and-file Shinigami and lower officers who oppose them. This lasts until Ichigo and Ganju, who landed together, encounter lieutenant Renji Abarai. Ichigo defeats him, alarming the Shinigami command enough that the captains themselves are sent out to pursue them. Another captain, Sōsuke Aizen, is found brutally murdered the next morning, sparking an internal conflict among the Shinigami, several of whom suspect other Shinigami officers of the murder.
Ichigo and Ganju are met by Kenpachi Zaraki, a bloodthirsty captain with the reputation of being unbeatable, as they are approaching Rukia's prison. Ichigo sends Ganju on to break Rukia out of jail, while he duels Kenpachi alone. Kenpachi and Ichigo fight until they are both nearly dead, both ultimately admitting defeat and collapsing. After the fight, Ichigo is healed by Yoruichi who then reveals that she is not a cat but a woman, and that she and Urahara are both actually ex-Shinigami.
Ganju reaches Rukia's prison, where he discovers that she is the Shinigami who killed his brother, Kaien. A flashback scene ensues, in which it is shown that Rukia killed Kaien only after his body had been completely taken over by a Hollow, but that Rukia still feels guilty for his death. They are interrupted by the arrival of captain Byakuya Kuchiki, who noticed the prison being opened. Byakuya defeats Ganju, but Ichigo comes flying to the rescue, and a brief battle takes place. Yoruichi arrives on the scene but knocks Ichigo unconscious to end the fight.
Yoruichi knocks Ichigo unconscious when he refuses to leave, and manages to escape Byakuya with Ichigo. After Ichigo regains consciousness, Yoruichi begins to train him to use his Bankai, the most powerful form of Zanpakutō. Renji later joins to train with them as well, bringing news that Rukia's execution date has again changed. Meanwhile, Uryū and Orihime are confronted by Shinigami captain Mayuri Kurotsuchi. Uryū battles him but is quickly disabled by the Shikai of Mayuri's Zanpakutō. Even after Uryū overcomes this with the Quincy technique Ransōtengai, Mayuri is still too much for Uryū, who is forced to remove his Sanrei Glove. Uryū then completely overwhelms Mayuri, even after Mayuri uses his Bankai, but is unable to finish him, as Mayuri escapes by turning himself into a liquid.
Meanwhile, Shinigami officers are fighting throughout Seireitei. Shinigami captain Tōshirō Hitsugaya confronts fellow captain Gin Ichimaru, whom Hitsugaya believes killed Aizen, and battles him. Ichimaru retreats after lieutenant Rangiku Matsumoto arrives. The next day, Kenpachi rescues Ichigo's comrades, but is stopped by Shinigami captains Sajin Komamura and Kaname Tōsen. Kenpachi manages to defeat Tōsen, even after Tōsen uses his Bankai. Elsewhere, Renji attempts to rescue Rukia, but is stopped by Byakuya. Renji, despite using his newly acquired Bankai, is defeated by Byakuya. Finally, Rukia's execution begins, but she is saved by Ichigo and sympathetic captains Shunsui Kyōraku and Jūshirō Ukitake.
While Rukia is spirited away by Renji, numerous Shinigami officers start to battle each other. Ichigo defeats three lieutenants that were pursuing Renji and is then engaged by Byakuya. Ichigo was about to die in the battle but his Hollow self takes control of him and attacks Byakuya with more powerful attacks. Ichigo then manages to retake control of himself in the battle. Using his Bankai, Ichigo manages to battle Byakuya on even footing, and narrowly defeats him. Kyōraku and Ukitake flee the execution area for a more secluded place to battle Captain-Commander Genryūsai Shigekuni Yamamoto. Yamamoto incinerates the surrounding area with his Shikai, and begins to battle his former students. Captain Suì-Fēng is similarly accosted by Yoruichi, her former mentor. In a tearful encounter, Yoruichi defeats her using the Shunkō technique, but was underestimated earlier because of her avoidance of battle for many years.
Hitsugaya, while searching the Central 46 Chambers, discovers that Aizen is alive, and is the mastermind behind the events that have transpired in Soul Society. Aizen then effortlessly defeats Hitsugaya and travels to the execution area. As Rukia has been sent there by Tōsen, Aizen's accomplice, Aizen extracts the Hōgyoku from her, despite the efforts of Renji, Ichigo and Captain Komamura. However, before Aizen can flee, the entire officer corps of the Gotei 13 stops him. However, the arrival of several Menos Grande enable Aizen and his accomplices to escape to Hueco Mundo. Ichigo and his friends then return to the real world, leaving Rukia behind on her request.