The game's adventure mode covers the original manga's chapter 245 to 450. Chapter 245, in addition to spearheading the start of a new story arc, also marks the beginning of the so-called "Part II" myth arc, adapted on television as Naruto: Shippuden. The main story that focuses on Naruto Uzumaki is told through 8 chapters, including a prologue section. Clearing them all unlocks an additional "fragment" chapter detailing Taka's failed capture of Killer Bee, based on several nonconsecutive manga chapters from 404 to 417.

The game's adventure mode covers the original manga's chapter 245 to 450. Chapter 245, in addition to spearheading the start of a new story arc, also marks the beginning of the so-called "Part II" myth arc, adapted on television as Naruto: Shippuden. The main story that focuses on Naruto Uzumaki is told through 8 chapters, including a prologue section. Clearing them all unlocks an additional "fragment" chapter detailing Taka's failed capture of Killer Bee, based on several nonconsecutive manga chapters from 404 to 417.