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In the Naruto manga, when Naruto is taking his Chuunin exam in the first half of the series, Orochimaru alters the seal on Naruto's abdomen somehow, making him a much less skilled ninja and generally affecting his chakra control.

Later, Jiraiya removed whatever Orochimaru did, allowing Naruto to do things like stand on water, etc.

What exactly did Orochimaru do (and, by extension, Jiraiya undo) that affected Naruto so? Why did this affect him?

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Naruto is a genin from Konohagakure, a member of Team Kakashi, and the third and current jinchūriki of Kurama, the Nine-Tailed Demon Fox.

The bijuu sealed with Naruto was held in place by linking Naruto's internal chi energy with that of the bijuu. As Naruto grew older he was able to utilize that link to his benefit, tapping the power of the Nine-Tailed Demon Fox. Being a descendant of the Uzumaki clan, Naruto inherited incredible stamina and vitality, which is further augmented by the Nine-Tails. According to Kakashi, Naruto's normal chakra level is at least four times of his own.

Naruto had always had poor chakra control due to the interaction of the bijuu chakra with his own. However, when Naruto's life was in danger the bijuu released chakra to Naruto to augment his considerable natural chakra. This would increase his strength, resistance to injury and give him incredible stores of chakra allowing him to create jutsu rarely seen due to their prodigious energy requirements. He later learns to harness this power at will.

Early in his career, Naruto effectively resists Orichimaru's giant snake jutsu using the chakra of the Nine-Tail Fox. Orichimaru, using the Five Elements Seal, blocked access to the chakra of the Nine Tales by disturbing the balance of the original seal. The odd number seal that Orichimaru used disturbed the even number seal used to orginally bind the jinchūriki.

Jiraiya, one of the legendary Sannin would later remove that seal, (considered to be a nearly impossible feat) releasing access to the chakra and teaching Naruto how to both harness the power and to eventually seal the power away behind a barrier preventing its escape and allowing Naruto to effectively tap the bijuu Kurame, without fear of releasing it.

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Been some time since I watched Naruto, but what I remember is that the fourth Hokage made the seal on Naruto in such a way as to channel the nine tail's chakra into Naruto. Orochimaru recognizes this, and interferes with this channel, making Naruto's chakra unstable.

  • Yes. As I recall, it had to do with mixing an even-numbered seal and an odd-numbered seal. After that, Naruto was unable to access the fox's power. – Jeff Jan 11 '12 at 13:44
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The ways in which Naruto needed to use chakra later required more than just consumption. They required consistent chakra output at controlled levels. So, while Naruto could consume large amounts of chakra, doing precise things was not easy since (as was said above) his normal dual chakra was being disturbed/interrupted.

Jiraiya removed Orichimaru's overseal so that Naruto could draw Kyuubi chakra for summoning jutsu, and for walking on water which required a more delicate use of chakra than walking vertically up a tree.

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Ochimaru made an extra seal to prevent the chakra of the nine tailed fox and Naruto's to mix, so that Ochimaru would'nt have an problem fighting with him. Later on Jiraiya a Sannin takes that extra seal out and teach's Naruto how to use the power of the nine tailed fox without releasing it.

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The seal placed on Naruto at birth was an 8-pointed seal, while the one placed on him later by Orochimaru was a 5-pointed seal. The combination of the odd-numbered seal over top of the even-numbered seal made the connection between Naruto's natural chakra and that of the Kyuubi unstable so that any time he attempted to use chakra at all he was not able to easily control the flow. Naruto himself was unaware of this, but Jiraiya noticed the double-seal during their training and realized that this was what was causing Naruto to have so much trouble with controlling his chakra. I have not read the manga, but I do know in the anime series Jiraiya briefly explains the conflict between the odd-numbered and even-numbered seals when he removes Orochimaru's.

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