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The old Naruto, Part I, is mainly to establish the setting and the characters, form bonds between them, and have Naruto earn the respect of others as he works towards becoming Hokage. Sasuke also goes from being an ally to being an enemy, while Gaara, goes from being an enemy, to being Naruto's friend. Orochimaru is the main villain in Part I, while Akatsuki is introduced but not elaborated upon. The night Sasuke's family was murdered by Itachi is also revealed.

The new Naruto, Naruto: Shippuden, is the sequel to Part 1, being 3 years after Naruto. Naruto has come back from training with Jiraiya and tries to bring Sasuke back, as well as fights the Akatsuki during Part II. The other Jinchuuriki like Naruto are revealed as Akatsuki hunts them down one by one. Orochimaru is no longer the main villain, but Akatsuki is. Naruto grows very much during Part II, in skill and in mind. He learns about Nature Manipulation and perfects the Rasengan, a jutsu the Fourth Hokage couldnt finish. He also uses the power of the Fox less because of its dangerous influence on him and the harm it brings to his friends. New characters are introduced in Part II, and characters from Part I are there still but some arent seen as much as others. Shippuuden manages to change the entire perspective of Naruto's plot because it reveals the history of what exactly happened during the Uchiha Massacre, why Itachi killed everyone, and the person who reveals it all is Madara Uchiha, the real villain of the story. Sasuke becomes one of the major villains when he learns this, as Madara tells him the truth of his clan's slaughter, which makes Sasuke aim to kill every single person in the Leaf Village. Meanwhile, after the death of Jiraiya by the Akatsuki's co-creator Pain, Naruto learns the ways of the toads and becomes a Sage. He defeats Pain and becomes a hero to the Leaf Village, earning everyone's respect. But Naruto is also changed forever, because Pain educates him on war, and how the peace of the Leaf village was brought about by the suffering of other nations. Naruto learns revenge and hatred plague the ninja world, and because he is revealed to be the Child of Prophecy, he carries on Jiraiya's will in working to bring peace to the world. Against the threat of Akatsuki, the Five Great Nations form a Shinobi Alliance, as Madara declares the Fourth Great Shinobi World War.

In Part II, the main theme is much more mature, and embraces the ideology of the Will of Fire. The old generation entrusts the future of the world to Naruto's generation, and Naruto seeks to stop war, hatred, and revenge and eradicate it from the world. He tells Sasuke that they are fated to battle each other, and he, as Sasuke's friend, will shoulder his burden of hatred.