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The Raikage directed the Hachibi to be imbued into several Kumo ninja. The Bijuu proved too much for the hosts, and went on rampages. This forced Sandaime and his son A to battle the beast and seal it away. Eventually Sandaime decided to imbue the beast in the body of the young Killer Bee, who would go on to be a blood brother with his son A.

After Kabuto joined forces with Akatsuki, he resurrected many dead ninja to fight at their side using Edo Tensei. Sandaime Raikage was dispatched along with Nidaime Mizukage, Nidaime Tsuchikage and Yondaime Kazekage.

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After his brother was captured by Akatsuki, Raikage became furious and dispatched a squad to track them down. He then called a meeting of the Five Kages to discuss taking care of the Akatsuki problem. When Uchiha Sasuke attacked the conference, Raikage sought revenge for his brother. He fought Sasuke and managed to deal several crushing blows to the young man. When Sasuke protected himself with Amaterasu, A shrugged off the fire and delivered another striking attack. With his hand no on fire with the undying flames, A was forced to chop of his left arm to prevent the spread of the flames. A short time later Zetsu and Tobi arrived to help spirit Sasuke away. Raikage was then chosen lead the new alliance of shinobi nations against Akatsuki. He then learned that his brother was actually alive. Furious he and his attendants left the conference and tracked Bee down. They arrived in time to see Akatsuki member Kisame moving to capture Bee. A and Bee then did a combination lariat technique which killed Kisame.

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After Kabuto joined forces with Akatsuki, he resurrected many dead ninja to fight at their side using Edo Tensei. This included the previous generation of the Mist Seven Swordsmen and Ameyuri. When the Edo Tensei ninja Gari and Pakura met the Third Division of the Joint Shinobi Army in battle, they summoned the other six members of the group to fight along Momochi Zabuza. Ameyuri was among the ninja who still had access to their original blades. When Zabuza used his Kirigakure jutsu to shroud the battlefield in mist, Ameyuri and the other ninja used their sword's abilities against their living foes.

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Rock Lee participated in the Chuunin exam with his teammates Neji and Ten-Ten. He made it to the preliminaries of the third round but was defeated by Gaara of the Sand. Lee was forced to use a Kinjutsu forbidden technique to try and beat Gaara, however he pushed his body beyond its limits and damaged his muscles. He was then further injured by the crushing jutsu of Gaara's, which badly damaged his bones.

After the match Lee was told he would be unable to become a ninja due to the extent of the injuries. When Tsunade returned to Leaf Village she examined Lee's injuries. She determined that surgery was possible to repair the damage, however, there was also a 50% chance the surgery could result in Lee's death. Lee decided fulfilling his ninja way was worth the risk so Tsunade operated on him. The surgery proved to be a success and Lee was able to continue his ninja training.

Lee then hurried after Team Shikamaru as they rushed to return Sasuke. Lee arrived just in time to assist Naruto fight Kimimaro. Unfortunately when Lee left the hospital he grabbed Tsunade's sake bottle instead of his medicine. When he ingested the sake he got inebriated and used Suiken to confuse Kimimaro. Though he managed to connect several times, Kimimaro began to get the upper hand, until Gaara arrived. Sent alongside his siblings to help the group, Lee watched as Gaara put Kimimaro away for good. The two young men also had the opportunity to connect and put the past behind them.

Lee and the rest would return to the village unable to save Sasuke. Over the following years Lee advanced his skills and his rank, passing the Chuunin Exam. Shortly after Naruto returned to the village after training with Jiraiya, a new mission came in. Gaara had been abducted by Akatsuki and Team Gai was sent to help Team Kakashi. Lee helped his team fight the faux-Kisame and also battled their doppelgangers. Fortunately Naruto managed to save Gaara and Sand ninja Chiyo gave her life to bring him back to life. Lee then returned to Konoha with his team to await their next mission.

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Rokubi and Utakata were captured by Akatsuki. Akatsuki then removed Rokubi from Utakata's body, killing the host.

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Roushi was defeated in battle by Kisame, who chose to take him on solo. Kisame admired his strength and powerful elemental fusion jutsu. After his defeat, the Yonbi was removed from his body, resulting in his death.