The game primarily focuses on adding content while still using its predecessor's engine. Support character returns for the first time since Naruto: Ultimate Ninja 2 and is now called at will (subject to meter restriction), rather than appearing from time to time; this will be the basis for the support system in the Storm series. The game also sees the return of collaborative Ultimate Jutsu from Naruto: Ultimate Ninja 3 and introduces collaborative normal Jutsu.
Master Mode starts with the Kazekage Rescue Arc and continues until the end of the Tenchi Bridge Reconnaissance Arc. Hero Mode has been removed, making this the the first game not to feature Part I story in any way, although Part I characters are still available.
Tropes exhibited by this game:
- And Now for Someone Completely Different: At different points in Master Mode, Naruto is replaced by Kankuro, Neji, and Sasuke, in that order, as primary character.
- Back-to-Back Badasses: The collaborative Ultimate Jutsu. Pairings include Naruto/Sakura, Sakura/Chiyo, Deidara/Sasori, Kisame/Itachi, and Orochimaru/Sasuke.
- The Cameo: Hidan, Kakuzu, Konan, Pain, and Zetsu all appear, albeit enveloped in shadow, during Gaara's Tailed Beast extraction.
- Evil Doppelgänger: The Wood Clone sidequest is about Tsunade attempting to create a new genjutsu, but ends up creating wood clones who take the form of existing ninja. Before they can wreak more havoc, she asks Naruto to dispose of them.
- Gameplay and Story Integration: In Master Mode, Naruto cannot access his Reversal Ultimate Jutsu until the Tenchi Bridge confrontation, as it transforms him into Four Tails.
- Gameplay and Story Segregation: Naruto's transformation to Four Tails does not destroy the Tenchi Bridge in the cutscenes, but come his battle against Orochimaru, the bridge is clearly seen destroyed in the background.
- How We Got Here: Master Mode starts with the climax of Tenchi Bridge Reconnaissance Arc, where Naruto, Sakura, and Yamato confront Sasuke in Orochimaru's hideout in Kusagakure. It ends when Sasuke is about to attack Naruto, at which point the scene cuts to the start of Part II.
- Loads and Loads of Characters: Expanding to Ultimate Ninja 4, the game adds 10 new characters, bringing the playable cast to 62.
- Party in My Pocket: Averted, unlike its predecessor. Master Mode is very RPG-like, with a party consisting of up to three main members and a backup. While you can only control Naruto or Sasuke inside encounters, the assists are there to help the fight. Outside encounters, you can freely switch Naruto with the others. Backups are this trope to the extent that they don't participate in encounters, but they contribute stat upgrades and are still selectable for clone fights.
- Secret Character: 12 characters are unlocked as you play through Master Mode's story. Part I characters are unlocked by defeating their clones in Master Mode, although if you have a Ultimate Ninja 3 save file, all of them are automatically unlocked.
- Sequential Boss: As with the manga, Sasori is fought three times in a row. His Hiruko puppet is the first to go, being destroyed by Sakura. The second time, Chiyo fights Sasori himself in a puppeteer match (she uses Dad and Mom's puppets, he uses the Third Kazekage's). The third time, Sakura takes over and fights Sasori's real form.
- Speed Blitz: Sasuke. His attacks even have a shadow effect to emphasize that yes, he moves like lightning. His Normal Ultimate Jutsu is possibly what he would inflict to Naruto after grabbing his shoulder had Sai not interfere in the manga's Chapter 308: he performs multiple incredibly quick sword slashes at his enemy to the point that they only notice them after he sheathes back his sword.
- Too Long; Didn't Dub: One of the few localized Naruto games with no English dub.
- Villain: Exit, Stage Left: In Master Mode, Orochimaru, Kabuto, and Sasuke simply abandon their Kusagakure hideout after battling Team 7.