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When Sand and Sound began their invasion, Raidou was struck by kunai to the chest and was taken out of the battle. He managaged to survive the battle however. Later, while on assignment, Raidou and Gemma confronted Orochimaru's Four Sound Gate Nins. Raidou was seriously injured but the medical attention of Shizune and Tsunade help treat his injuries.

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Shikaku and the Ino Shika Cho group get back together to help Hidden Leaf turn back the Sound and Sand invasion. Later on Shikaku goes with his son to get his promotion to Chuunin. It is during this period Shikaku teaches his son the Kageshibari no Jutsu.

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Though Shikamaru appears a young man bored with life and his job as ninja, he holds a firm respect for his job and his duty to protect his friends and teammates. And though he is lazy and had low grades at the Ninja Academy, Shikamaru is highly intelligent with an I.Q. of over 200. A young age he became friends with Akimichi Chouji, and their friendship would extend later into life as teammates in Team 10 under their Jounin sensei Sarutobi Asuma. Shikamaru would rather relax and look at the clouds, than expend any energy doing school work. His general desire is to make a good living and be able to retire, successful and happy with himself.

Shikamaru studied under his father Nara Shikaku and learned many of the kage (shadow) manipulation jutsu. As the years passed, Shikamaru has added many shadow attack variations to his arsenal. Shikamaru's mother wanted the best for her son and pestered him constantly, which led him to be cynical of women and their supposed bossiness. His troubles with women would extend to many of the battles he faced, having to combat Tsuchi Kin, Temari and Tayuya. His testy relationship with Temari would extend over the years, with the two ninja becoming friends. Though Naruto would accuse the two of being something more than friends, both Shikamaru and Temari would deny such a relationship.

Alongside his team Shikamaru participated in the Chuunin Exam. After the third test preliminaries and the final third test itself, he was the only one to be acknowledged as worthy Chuunin material. From this point on he was able to don the Chuunin flak jacket with honor. Though the mission to return Sasuke failed and Shikamaru felt horrible for the near deaths of his team, the words of Temari and his father helped him realize that if he stopped being a ninja, someone else would have to look out for his friends instead. This caused him to reevaluate his feelings and reaffirm his desire to become a better ninja.

Over the next years Shikamaru would further develop his skills and be selected as a Chuunin Examiner when the exam returned to Konoha. Alongside Sand kunoichi Temari who acted as an advisor, they would begin preparations for the new exam.

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In addition to being Tsunade's brother, he was also the grandson of the First Hokage. Nawaki expressed a desire to become the Hokage himself one day as well. Tsunade gave her little brother their grandfathers pendant on his birthday. The next day Nawaki died in battle. After Tsunade also lost her boyfriend in battle. Because her boyfriend Dan also wanted to be Hokage, she felt that dreaming of becoming Hokage led one to take foolish actions.

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Little is known about the Nibi and its abilities. In mythology the two-tailed cats were said to have the ability to manipulate the dead like puppets and have been associated with strange fires and occurrences. Nibi has been shown to use fire in its attacks and its nickname brings to mind the dead manipulation abilities.

Akatsuki members Hidan and Kakuzu were charged with capturing the Nibi. They managed to defeat Yugito in battle and extract the demon from her body, killing her.

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Though highly skilled in using her Jinchuuriki abilities, Yugito was defeated in battle. When Hidan and Kakuzu gave chase, she fled; leading them to what she thought was a well designed trap. In an abandoned industrial complex, she destroyed the exits to prevent their escape. After she transformed into her Jinchuuriki form, she began to attack. Unfortunately the skills of the Akatsuki duo proved too much and she fell in battle. Yugito was then taken back to Akatsuki's base by Zetsu. There the Nibi was removed from her body, killing her.

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Rin and her teammates were ordered to destroy a bridge during a war against Hidden Rock some 13 years before the start of the series. When they embarked on their misson she and her team celebrated Kakashi's advacement to the rank of Jounin. To celebrate, she gave Kakashi a medical pack as a gift and the Fourth Hokage gave him a special kunai. To her surprise she learned Obito had forgotten to get anything for Kakashi. The Fourth Hokage told the team Kakashi would be their leader on their mission because he had to go elsewhere to lend support to fellow Leaf ninja already in battle.

On their way to their destination, the trio was attacked by Rock-Nins and Rin herself was kidnapped. Obito was determined to rescue Rin but Kakashi was more focused on completing the mission. Appealing to Kakashi's feelings for his father, Obito managed to sway Kakashi into helping him. While tracking them down, Obito fought one of the Rock ninja and managed to activate the Sharingan he had so desperately wanted. Unfortunately Kakashi injured his left eye in the battle. Obito and Kakashi then found Rin's location and saw she was under a genjutsu spell. The enemy ninjas were attemping to gather military information from her so the Leaf ninjas attacked and overcame the Rock ninja. Unfortunately the ninja was not knocked out and he caused an earth jutsu to crush Obito.

Obito asked Rin to do him a favor. Perform an operation to give Kakashi his left eye. Obito knew his body was crushed and he had no chance for survival, so he asked Rin to help him give Kakashi a gift since he had forgotten to before. Crying, Rin agreed and the present Kakashi was born. With the new Sharingan eye in place, Kakashi was able to fully utilize the Chidori and avoid counter attacks. As Rock reinforcements came, Kakashi and Rin had to flee leaving Obito behind. Rin learned that Obito had loved her but she was unable to return the feelings because she was always enamoured with Kakashi and never knew of Obito's love until it was too late. As Kakashi and Rin became surrounded, Kakashi attempted to use the Chidori but passed out because he had used all his chakra. Rin used the Hokage's gift to Kakashi, a special teleportation kunai which brought him to their location for support. The Fourth Hokage was able to arrive in time and save the pair. Rin, Kakashi and the Fourth Hokage were able to go on and destroy the bridge.

Unknown to Rin, Obito had been saved by Uchiha Madara. When Obito learned that Rin and Kakashi were in danger from Hidden Mist ninja, he rushed to their aid with the help of a White Zetsu clone. He then watched in horror as Kakashi killed Rin with Raikiri for some unknown reason. This act awakened the Mangekyou Sharingan in both men. Kakashi passed out and Obito then slaughtered the gathered Hidden Mist ninja who sought Rin's body for some reason. Rin was eventually memorialized with a marker in Konoha. It was upon that spot that Obito, then acting as Tobi, summoned the Kyuubi for its attack on Konoha during Naruto's birth. The memory of reviving Rin in world of peace was also what fueled Obito to help carry out Uchiha Madara's plan to cast Infinite Tsukuyomi on the world.