The 2D game system is retained with several changes, most notably a condition-based Ultimate Jutsu. The graphics have been overhauled and takes more cue from the anime, rather than the manga. The sandbox-like Ultimate Contest has been replaced by the action-adventure Master Mode, where the player controls Naruto to explore various locales, complete quests, and battle enemies.
Master Mode starts with a filler story called the "Black Shadow" arc, followed by Part II chapters from 245 to 260 of the Naruto manga. Despite focusing on Part II, the game includes a condensed version of Part I storyline in the form of Hero Mode, similar to Hero's History from Naruto: Ultimate Ninja 3, and Part I characters are still available. Note that Kakashi Gaiden (c. 239-244) is not featured in any capacity, outside of the return of the Yellow Flash.
Tropes exhibited by this game:
- Asleep for Days: Naruto states in his narration that after defeating the Black Shadow, he collapsed and did not wake up for a week.
- Canis Major: The Black Shadow's true form is a gigantic two-headed wolf.
- The Cameo: Pain, the leader of the Akatsuki, appears in the post-credits scene.
- Compressed Adaptation: Much like Hero's History, Hero Mode is a recap that tells the abridged version of Part I interspersed with the occasional battles. To access them, collect memory orbs from Master Mode. The retelling is a bit more in-depth than the extremely bare bones Hero's History, however.
- Dug Too Deep: A variation. The Black Shadow was once repelled from attacking the village by flowers that grew around a tree located in front of the cave. However, centuries ago, the tree was cut down to free up space for the villagers to transport crystals mined from the cave. As a result, the village no longer have no natural protection from the Black Shadow, who threatens to destroy the village unless they sacrifice a human every few years.
- Filler: The Black Shadow arc, centering on the seasonal Human Sacrifice of the Tree Felling Village to appease the titular Black Shadow. It takes place sometime during the two and a half year timeskip between Part I and II.
- Gameplay and Story Integration: Throughout the entirety of Hero Mode, Part I Naruto cannot access his Reversal Ultimate Jutsu, because it transforms him into the One-Tailed awakening form, which he canonically does not enter until the tail end of the story. He still does the Normal Ultimate Jutsu even when his HP is below 50%.
- Heads I Win, Tails You Lose: Even after he defeats him during the fight above Sunagakure, Gaara still gets kidnapped by Deidara. Likewise, Kankuro ends up becoming poisoned after his fight against Sasori.
- Human Sacrifice: The Tree Felling Village send a person every few years as sacrifice to appease the Black Shadow, who in return "protects" the village by refraining from destroying them. Aoi is the latest person who undergoes this torment, although it is revealed that she does so willingly.
- Limit Break: This time, each character has a fixed set of Ultimate Jutsu that changes when certain conditions are met. At the start of a battle, they can access the Normal UJ. If their health is below 50%, the UJ will change into Reversal, which either deals a huge damage (up to 50% of total HP if done right), activates awakening form, or both. Finally, if a character enters their awakening mode, the UJ will change into Awakening UJ, which uniformly does a maximum of about 40% of total HP damage.
- No Ending: The game ends abruptly in the middle of the Kazekage Rescue Mission arc after Naruto defeats Fake!Itachi, with him and the others discussing Naruto's determination to save Gaara. Meanwhile, Deidara and Sasori successfully deliver Gaara to the Akatsuki Hideout, where the Akatsuki begin the Tailed Beast extraction.
- Old Save Bonus: Having an Ultimate Ninja 3 save file nets you 100,000 ryo and unlocks all Part I characters with the exception of the Yellow Flash.
- Our Zombies Are Different: In the cave of the Tree Felling Village, Naruto faces reanimated bodies of people who died in the cave.
- Panacea: The flowers growing around the tree that once grew in front of the cave in the Tree Felling Village was able to cure any disease.
- Party in My Pocket: Sakura, Kakashi, and Chiyo are nowhere to be seen in the overworld when they accompany Naruto to save Gaara, only to suddenly appear in the cutscenes.
- Secret Character: Chiyo, Deidara, Itachi, Kisame, and Sasori are unlocked by playing through Master Mode. There are also several missing Part I characters who can be unlocked by playing through Hero Mode, although if the player has an Ultimate Ninja 3 save file, everyone except the Yellow Flash will be automatically unlocked. Once everyone is unlocked, the Yellow Flash will be made available.
- Sins of Our Fathers: The ancestors of the Tree Felling Village cut the tree that grew in front of the cave, which caused the evil-repellent flowers to wilt, resulting in the village becoming the Black Shadow's easy prey.
- Took a Level in Badass: As with the manga, the timeskip gave all genin characters a major upgrade in power. Special mention goes to Sakura, who went from being a generic taijutsu practitioner into a very potent medic nin with strength comparable to Tsunade.