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After the preliminary match-ups, there was a one-month period in which the remaining Genin could prepare themselves. Various dignitaries were also invited to watch the main matches. During this month, Naruto met Jiraiya, another Sannin, for the first time. Jiraiya agreed to be his sensei, and was the one who taught him most of the advanced techniques he learned during that time.

Under Jiraiya, Naruto improved his chakra control by practicing walking on water, learned how to call upon the demon fox's energy at will after Jiraiya used a counter seal to cancel Orochimaru's sealing technique, and how to use a summoning technique to call the giant toad, Gamabunta, to his aid, but was exhausted after completing his training, and Gamabunta carried him to the hospital.

Also, during the month of training, Dosu who was trying to sneak up on, and kill Gaara was ripped to shreds by him. Hayate Gekkō (the third exam proctor) was murdered by Baki, the Jōnin of Gaara's squad, Team Baki, after he overheard Baki talking with Kabuto about their plans to invade Konoha. Gaara also attempted to assassinate Rock Lee in the hospital on the day before the finals, but was stopped by Naruto and Shikamaru. Gaara revealed his past, which led to Naruto realizing that they had similar histories of prejudice, before Guy stepped in and forced Gaara to leave.

Naruto's fight with Neji a month later in the first match of the finals was a very dramatic one. During the fight, Neji lectured Naruto much as he had done with Hinata during the preliminaries, telling Naruto that dropouts remain dropouts and that this cannot change. Naruto eventually won the battle through a combination of the demon fox's power sealed within him and sheer belief in victory. In the process, he changed Neji's outlook on life, and inspired him to create his own fate, thus forming another important bond. Naruto was able to make Neji understand that destiny can be changed, and they became good friends from that point on.

The second match, which featured Sasuke versus Gaara, was moved to be the last, as Sasuke hadn't shown up yet. Normally he would have been disqualified on the spot, but his match had been highly anticipated – in fact, some of the crowd commented they had mostly come just to see him fight, forcing the Third Hokage to give into the Kazekage's request to postpone the match.

The third match, which featured Shino versus Kankurō, was given to Shino on default, since Kankurō forfeited to "keep his techniques a secret" before the invasion plan was launched.

The fourth match was Temari versus Shikamaru. Both Temari and Shikamaru were excellent strategists, but Shikamaru was better. Although it appeared throughout the match that Shikamaru was using pointless attacks, he was actually five steps ahead, and managed to skillfully manipulate Temari into a position where he could attack from behind, using the tunnel which Naruto had dug during his match with Neji to stealthily extend his Shadow Imitation Technique. This took control over Temari's body, and forced her to imitate every one of Shikamaru's movements. Although Shikamaru could have won, he quit instead, saying that he was too low on chakra. His real reason for quitting, however, seems to be because he is incredibly lazy and saw no point in winning, which would only lead to having to fight in further matches. He also didn't want to hurt a girl.

Gaara versus Sasuke came around again. This was the battle that the crowd had been looking forward to. Sasuke arrived late, but the waiting time was extended again because of the importance of the match. Sasuke demonstrated that his speed had vastly increased, to the point where the sand guarding Gaara could not keep up. Sasuke also demonstrated the Chidori, a technique he had learned from Kakashi, which also happened to be Kakashi's only original jutsu, to injure Gaara. Before the match could finish, however, a smoke bomb was set off in the Hokage's box. Kabuto, who was actually working for Orochimaru, used a Genjutsu to put almost everybody in the crowd to sleep, and the Invasion of Konoha commenced.