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After his parents were killed, Yahiko met two other orphaned children, Konan and Nagato. While on their own, the trio would do what they could to survive. One day they met the Sannin, who were returning to Konoha after the end of the war with Rain. Yahiko asked the Sannin for food and begged the Leaf to teach them Ninjutsu. Orochimaru suggested killing the youth then and there, as their life would only be filled with pain in the future. Jiraiya said absolutely not, and offered to look after them for awhile. After settling in to a small cottage, Jiraiya began to feed and watch after the children. When Nagato began to imagine how much like his family life his new surroundings were, Yahiko yelled at him in anger to man up, as crying gave off a bad impression of Rain country boys. Yahiko went on to argue that the only way for the conflict surrounding Rain to end, would be if everyone experienced the same pain they went through. Yahiko promised to protect his friends and reiterated his request for Jiraiya to train them.

Later that night Yahiko and Nagato were attacked by a refugee from Hidden Rock. Nagato used his Rinnegan in self-defense and quickly killed the attacker. Jiraiya was shocked by the appearance of the legendary Doujutsu and finally agreed to train them. Over the next three years Jiraiya taught the youth Ninjutsu. When the trio finally managed to defeat one of his Kage Bunshin, he let them know their training with him as ended. He wished them well and the trio remained behind to do what they could to help their country. The orphans would fight many battles and Yahiko would apparently fall in one such conflict. Konan and Nagato would continue on with their goal of changing Rain and the world, as Akatsuki members. Nagato himself would change his name to Pain and make his life goal to honor Yahiko's desire that the world feel the same pain they once felt.

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Though he wears the head protector of Leaf, Kabuto is actually a spy for Hidden Sound. Kabuto acts as the second in command to Orochimaru's army. When Kabuto was young, he was found alone by a Leaf medical Jounin after the battle of Bellflower pass. Though he was the child of the enemy, this man would go on to adopt and raise Kabuto as his own. During this time he taught Kabuto many medical techniques and jutsu. It is said that Kabuto's skill and ability rivals that of Hatake Kakashi.

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Like the other members of his clan, Fuu specializes in mind/body manipulation. When Danzou fled the summit, Fuu remained behind to help recover a Byakugan eye which had been stolen and implanted in the past in Mist ninja Ao. Fuu used his jutsu to take over Ao's body and place the Mist ninja's mind into that of a puppet. Before Ao could successfully cut off Ao's head for later retrieval, he was caught by the Mizukage. The Mizukage deduced Ao was not himself and successfully removed Fuu from Ao's body, ending the jutsu. Having failed, Fuu travelled on with Danzou and Torune. When the trio were confronted by Uchiha Madara in the guise of Tobi, the Root members moved to attack. Every attack the duo tried was phased through and neutralized by the elder Uchiha, who eventually also phased Fuu and Torune out of existence as well.

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Ino and Sakura weren't always rivals. When they were little young, Sakura did not have much self-confidence in herself. It wasn't until Ino became friends with her and encouraged her to not be afraid of the taunts of the other children that Sakura grew out of her shell. Their friendship ended though when they both took an interest in Sasuke. Their rivalry came to a head in the third prelimiary round of the Chuunin Exam, as the two young women were placed against each other in fight. Both gave it their all but in the end there was a double knock out. This resulted in both Ino and Sakura being unable to move on to the third round.

Ino would later watch her teammate Shikamaru in the Exam's third test. She was excited and hoped he would knock out his opponent Temari. When he quit his match for tactical reasons she was shocked. She was later rendered unconscious when Kabuto put the stadium audience to sleep. Over the following years Ino would greatly increase her skills and eventually pass the Chuunin Exam. After Naruto returned from his training with Jiraiya, she welcomed him back. Ino would later take a fancy to Naruto's new teammate Sai. The socially clueless Sai always said what was on his mind. When he called Sakura ugly she made him pay for it. When he met Ino he decided he should say the opposite, calling her beautiful. The blushing Ino didn't know what to say.

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Inoichi and the Ino Shika Cho group get back together to help Hidden Leaf turn back the Sound and Sand invasion.

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When Sand and Sound began their invasion, Aoba was able to avoid Kabuto's Genjutsu spell and helped fight at the arena after the third test of the Chuunin Exam. Aoba later made the mistake of eagerly rushing to Kakashi's apartment to tell him Uchiha Itachi had returned to the village. Little did he realize that Sasuke was there visiting his sensei. Overhearing Aoba's excited news the enraged Sasuke then took off in pursuit of his brother.

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Yamato, whose real name is Tenzou, was an elite ANBU recommended by Kakashi himself for the mission. Yamato would leave behind his ANBU mask and gear and wear his flak jacket. Yamato wears a forehead protector similar in style to Nidaime Hokage. A further connection to the brothers Shodai and Nidaime Hokage was seen when he used a Mokuton (Tree Release) technique to threaten his team to calm down and stop their infighting.

Yamato is connected to the legacy of Shodai because he carries his genes within him. When Orochimaru was still a respected ninja within Konoha, he carried out experimental gene therapy on 60 village children. Orochimaru sought to gain Shodai's Mokuton and Bijuu controlling powers for his own. To that end he obtained genetic material and spliced it into 60 children. Orochimaru soon left and never saw the fruit of his labors. All but one of the children died. Yamato managed to survive and grow into a powerful ninja.

Yamato would get his chance to meet his "maker" on the bridge in the Grass Country. When Kabuto appeared alongside Orochimaru in the hopes of killing Sasori, Yamato and his team were given the opportunity to take out Orochimaru for good. When Naruto began to rampage in his tailed Kyuubi form, Yamato used another Shodai ability in controlling the bijuu. He was able to calm Naruto's wild mind and return him to normal. His group then pursued Orochimaru thanks to a tracking seed placed in Sai. Though they successfully infiltrated Orochimaru's compound and found Sasuke, the meeting did not last long. Before Yamato had a chance to get serious, the Sound ninja fled.

Yamato and his team returned to Konoha. They were given a new mission by Tsunade and further built their team dynamics. After the mission, Yamato would assist Kakashi in Naruto's new training regimen. By managing Naruto's Kyuubi powers, Naruto was able to use Tajuu Kage Bunshin and greatly reduce his training time. And with Yamato's Earth, Water and Wood elemental styles, he was able to further teach Naruto how to develop his own unique elemental jutsu.

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Yashamaru was Gaara's uncle, the brother of Gaara's mother. Yashamaru watched as his sister had the spirit of a dead Sand priest imbued into her unborn son. After she died her husband the Kazekage directed Yashamaru to watch over Gaara. Though Yashamaru tried to teach Gaara the nature of love, he still resented Gaara because he felt he was responsible for his sisters death. When Gaara proved to be uncontrollable, the Kazekage ordered him assassinated. One of the assassins ordered to kill Gaara was Yashamaru. When he attempted to kill Gaara, Gaara's sand protected him and injured Yashamaru. When Gaara saw it was his caretaker he was unable to believe that he had tried to kill him. Yashamaru told Gaara that the Kazekage had ordered him to kill Gaara. Gaara took some hope in that, saying that it was okay if it was under orders. But then Yashamaru told Gaara that he would have tried to kill him even if he wasn't ordered to. As he lay there dying Yashamaru told Gaara that he always hated and resented him for killing his sister. When one final strike he attempted to use an exploding note to kill Gaara. Though the sand protected Gaara, the emotional impact was the last straw that sent him over the edge. From that day on he would fight only for himself and kill all those who would threaten his existence.

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The Yonbi and Roushi were defeated in battle by Hoshigaki Kisame. Akatsuki then removed the demon, killing Roushi.

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After Kurenai was assigned her Genin team, she went to the Hyuuga family head Hiashi to ask if it was okay that the family's heir would be putting her life on the line everyday. Unimpressed with Hinata's progress, Hiashi dismissed his daughter’s abilities. Kurenai was surprised but she accepted his response. She then kept a watchful eye over Hinata, noting how she did poorly on their team missions. When Hinata later pushed herself more than ever before in the Chuunin Exam, Kurenai was greatly impressed by this newfound strength. When Neji was later enraged by Hinata's words, Kurenai jumped in alongside other Jounin masters to stop the young man.

Over time Kurenai would develop a close relationship with fellow Jounin Sensei Sarutobi Asuma. Though she would deny they were dating, the two did develop a bond. When Uchiha Itachi returned to the village, she did her part to subdue him. When she became endangered, Asuma jumped in to help. With the arrival of Might Guy, Itachi and his partner Kisame fled.

Over the next several years Kurenai would further train her students and watch as they finally passed the Chuunin Exam. Her relationship with Asuma would grow. With the grave dealings of Akatsuki coming to the forefront, Asuma would think over his place in Konoha and his relationship with Kurenai. When he was called away to track Akatsuki down, he made one final stop by Kurenai's apartment. He could not bring himself to talk to her though, by the time she noticed someone outside, he was gone.

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Little does Yuura know that he has been placed under a memory block jutsu for over a decade. This block was placed by his former master Sasori of the Red Sands, the master of puppets in Hidden Sand. The block made Yuura forget that he was actually gathering data and serving as a plant to wipe out the Sand's defenses. When Sasori returned as a member of Akatsuki to Hidden Sand, he activated Yuura and removed the memory block. Returning to his masters commands, Yuura wiped out the Sands defenses, allowing them easier access to capture Gaara.

Later Yuura and another individual were sacrificed for the Akatsuki's leaders Shouten no Jutsu. An image changing technique which allows an Akatsuki member to take control of the body and use it as if it was their own. The sacrifice would change to look like the member and utilize however much chakra the member was willing to donate to them. The body essentially would become the Akatsuki member, but it would be prevented from using any of their bloodline techniques. Yuura was used as a stall mechanism. Uchiha Itachi used his body to delay Naruto and his team from rescuing the captured Gaara from the clutches of Akatsuki. The combined attacks of Kakashi and Naruto managed to kill the "Itachi" and reveal the fallen Yuura. Zetsu later ate his body for sustenance.