The students at the Ninja Academy, where the story begins, are split up into teams of three after their graduation and become Genin, or low-class ninjas. Each team is assigned an experienced sensei, or teacher. These core teams form a basis for the characters' interactions later in the series, where characters are chosen for missions for their team's strength and complementary Sasuke Uchiha, and their sensei Kakashi Hatake, also called the "copy ninja" for copying thousands of ninja techniques with his eye, forming the core of his world-in-the-making. The other three-man teams of his former classmates form another such layer, as Naruto connects with them to various degrees, learning of their motives, vulnerabilities and aspirations and often relating them to his own. The groups of threes is not limited to the comrades Naruto's age – groups in the story in general come in threes and multiples of three with very few exceptions. skills; Naruto's Team 7 becomes the social frame where Naruto is acquainted with and Sensei-student relationships play a significant role in the series; Naruto has a number of mentors with whom he trains and learns, most notably Jiraiya and Kakashi Hatake, and there are often running threads of tradition and tutelage binding together several generations. These role models provide guidance for their students not only in the ninja arts but also in a number of Japanese aesthetics and philosophical ideals. Techniques, ideals, and mentalities noticeably run in families, Naruto often being exposed to the abilities and traditions of generation-old clans in his village when friends from his own age group demonstrate them, or even achieve improvements of their own; it is poignantly noted that Naruto's generation is particularly talented.

Many of the greater lingering mysteries of the series are questions of character motives and identity. The legacy of Naruto's parents, the goals that guide Kabuto Yakushi, the objective of the mysterious organization Akatsuki and the identity of its mysterious leader – these are only a few of the fundamental unanswered questions of "who" and, by proxy, "why" currently at the core of the series. The story is remarkably character-driven; the theme of causality runs inherently throughout the series as characters reciprocate for their past actions and relationships.

In this respect, characters' respective destinies are very much intertwined, and large emphasis is placed on comradeship and 'bonds' between the community or individual. Character names often borrow from Japanese myth and literature (such as the names borrowed from the folk-tale Jiraiya Goketsu Monogatari), or are otherwise elaborate puns (see Hinata Hyuga); often there is a noticeable influence of the story behind the name shouldered by the character.