Naruto's final battle with Sasuke had a huge impact on him to say the least. He's obsessed with getting strong enough to not just battle the Akatsuki but to rescue Sasuke from Orochimaru.
When he returns to the village, everyone can't believe how much he's grown, but Naruto quickly discovers that although he is much stronger, he is now very far behind his classmates. Like him, they've continued to study and get stronger, but unlike him, they have been able to take the exams and have now progressed from Genin to Chunin.
Naruto barely has time to settle in before Tsunade is sending him on missions with Sakura and Kakashi. Before they know it, Naruto, Kakashi and Sakura are battling the Akatsuki in a race to save the Sand Village Kasekage, Gaara.
In a battle, Kakashi overused his sharingan and ends up in the hospital. To keep the team going on missions Tsunade has to make a very important decision. Who will head team Kakashi? She decides that Yamato will be the best choice. Yamato is chosen for many reasons, not the least of which is he's a member of the Onbu Black Ops team.