The game is a 2D fighter, like its predecessors. It further refines the battle system and introduces the concept of customizable Ultimate Jutsu. Assist characters have been removed, making it the only game in the series to do so. The exploration mode introduced in Naruto: Ultimate Ninja 2 has been expanded into an open world system, where you can travel through a condensed map of the Land of Fire. This mode tells an original story, while the manga canon is told through the recap-like Hero's History.
The game follows Naruto's manga canon from the beginning up to the end of the Sasuke Recovery Mission Arc (chapter 238).
Followed by a sequel called Naruto Shippuden: Ultimate Ninja 4.
Tropes exhibited by this game:
- Adapted Out: Kankuro and Temari don't appear to assist Kiba and Shikamaru during their fight against Sakon and Tayuya, respectively.
- Ascended Extra: Hinata's younger sister, Hanabi, is a playable character and can be interacted with in Ultimate Contest. She is rather cold when Naruto first talk to her, but gradually opens up as they spend time together.
- Attack of the 50-Foot Whatever: New to the series is the Summoning Battle, in which a specific character performs Ultimate Jutsu to summon or transform into a gigantic beast. They gain an advantage over their opponent, as being humongous they are invulnerable to most attacks and have to be attacked by jumping in their direction first. The beasts include Gamabunta (Naruto and Jiraiya), Inner Sakura (Sakura), Giant Choji (Choji), Two-Headed Wolf (Kiba), Shukaku (Gaara), Manda (Orochimaru), and Katsuyu (Tsunade).
- Betting Minigame: Three-Way Deadlock returns (now called "Three-Way Deadlock 2") and features the same rules as Ultimate Ninja 2. New to the game is "Leaf Story", which is much the same but has interactive bonus rounds, is more expensive to play, but rewards you more.
- Cheat Code: There is an internal cheat that unlocks all playable characters in the game sans Hanabi and the Yellow Flash.
- Compressed Adaptation: The Hero's History mode, in a nutshell. Every arc prior to the Sasuke Recovery Mission is condensed into four chapters, each containing either one or two battles. The Chunin Exams arc, which in the manga is a Tournament Arc basically designed to show off the Konoha 12's abilities, has been reduced to two battles: Naruto vs Orochimaru in the Forest of Death, and Naruto vs Neji in the Chunin Exams Stadium.
- Defeat Means Playable: In Hero's History, most characters are unlocked by beating them in the chapter they are featured in. In Ultimate Contest, Anko, Asuma, and Kurenai are unlocked by beating them during the crystal contest.
- Filler: The Ultimate Contest tells an original story involving a contest where Konoha and Suna ninja compete for crystals to earn a special prize.
- Giant Spider: Kidomaru can summon one. Also, the aptly titled Forest of Giant Spider location has Kidomaru's spider lurking about in the background.
- Heads I Win, Tails You Lose: The climax of the crystal contest. Despite Naruto giving all he has, Kakashi still ends up knocking him flat. However, Kakashi decides to forfeit after seeing how persistent Naruto is.
- Joke Character: Konohamaru. His moves are limited and gimmicky, he runs with Wheel o' Feet, and one of his jutsu is Sexy Jutsu. Even his Ultimate Jutsu doesn't take itself seriously.
- Minigame: There are Lee's Workout Challenge (including push-up, jump, and strike-a-pose), Sakura's Tree Climbing, and Tenten's Target Practice. Three-Way Deadlock returns and is joined by a new pachinko, Leaf Story.
- Old Save Bonus: Having the save file for Ultimate Ninja 2 gives you 607 Ninja Info Cards and 50000 ryo.
- One-Winged Angel: Permanent awakening forms make a return for the first time since Ultimate Ninja. Successfully performing a certain Ultimate Jutsu will transform a character until the end of the battle. There is no significant increase in stats, but their movelist changes completely. Characters who have this ability are Naruto, Sasuke, Lee, Choji, the Sound Four, Kimimaro, and Gaara.
- Post-End Game Content: Clearing the main story for Ultimate Contest unlocks Anbu Kakashi and the Green Beast as playable characters. It also opens up many sidequests, including those that unlock Hanabi, Konohamaru, the First Hokage, the Second Hokage, and the Yellow Flash.
- Promoted to Playable: Asuma, Jirobo, Kidomaru, Sakon, and Tayuya, among previous support characters. The game also adds Anko, the First Hokage, Konohamaru, Kurenai, the Second Hokage, and the Yellow Flash, among background NPCs in the previous games.
- Reality Ensues: In the ending for Ultimate Contest, Naruto gets to be Hokage for a week... only to find out that it mainly consists of paperwork, which still tires him, because there are a lot of them. Also, Tsunade only gives him the job for a week because, no matter how hard he strives to be Hokage, he is still an immature and inexperienced kid.
- You can trigger social/dating sidequests with most playable characters in Ultimate Contest by giving them a specific item. Do this two times and they will give jutsu in return (or in the case of Hanabi, the right to use her as a playable character).
- To unlock Konohamaru, talk to Udon and Moegi in the Ninja Academy and answer a series of Pop Quiz. Once you unlock him, you can talk to Ebisu and answer another set of Pop Quiz to unlock the First and Second Hokage.