Naruto Uzumaki (Playable in Part I and Part II) (One-Tailed Form, Nine-Tails Chakra Mode (Hokage Costume, Samurai Costume, Goku Costume)
Sage Naruto (Six-Tailed Form)
Sasuke Uchiha (Playable in Part I and Part II) (Sharingan, Curse Mark Mode, Susanoo Mode, Susanoo Eternal Mangekyō Sharingan Mode (Road to Ninja Costume, Kimono Costume)
Sakura Haruno (Playable in Part I and Part II) (Allied Shinobi Forces, Maiden's Anger Mode, Herculean Mode (Swimsuit Costume, School Uniform Costume)
Kakashi Hatake (Allied Shinobi Forces, Sharingan Mode) (ANBU Costume)
Young Kakashi (White Light Blade Mode)
Yamato (Wood Style Mode)
Sai (Allied Shinobi Forces, Fast Writing Mode)
Shikamaru Nara (Allied Shinobi Forces, Strategy Mode)
Ino Yamanaka (Allied Shinobi Forces, Hundred Scattered Flowers Mode)
Chōji Akimichi (Allied Shinobi Forces, Butterfly Mode)
Rock Lee (Playable in Part I and Part II) (Eight Gates Mode)
Tenten (Allied Shinobi Forces, Bashōsen)
Neji Hyūga (Playable in Part I and Part II) (Allied Shinobi Forces, Byakugan Mode)
Shino Aburame (Allied Shinobi Forces, Beetle Mode)
Hinata Hyūga (Playable in Part I and Part II) (Allied Shinobi Forces, Byakugan Mode, Twin Lion Fists Mode)
Kiba Inuzuka (Allied Shinobi Forces, Food Pills Mode)
Might Guy (Eight Gates Mode)
Hashirama Senju (Wood Release Ninjutsu Mode)
Tobirama Senju (Water Release Ninjutsu Mode)
Hiruzen Sarutobi (Hokage Mode)
Minato Namikaze (Yellow Flash Mode)
Tsunade (Herculean Mode) (Swimsuit Costume)
Jiraiya (Sage Mode)
Gaara (Playable in Part I and Part II) (Allied Shinobi Forces, Brutal Sand Mode, Kazekage Mode)
Temari (Allied Shinobi Forces, Heavenly Fan Dance Mode)
Kankurō (Allied Shinobi Forces, Salamander Mode)
Killer B (Samehada, Gyūki)
A (Raikage Mode)
Darui (Black Lightning Mode)
Ōnoki (Tsuchikage Mode)
Mei Terumī (Mizukage Mode)
Mifune (Samurai Mode)
Danzō Shimura (Released Seal Mode)
Obito Uchiha (Sharingan Mode)
Tobi (Masked Man, Fourth Shinobi World War) (Sharingan and Rinnegan Mode)
Itachi Uchiha (Tsukuyomi Mode) (Reincarnated)
Kisame Hoshigaki (Samehada Fusion Mode)
Orochimaru (White Snake Mode)
Kabuto Yakushi (Chakra Scalpel Mode, Snake Mode)
Kimimaro (Curse Mark Mode)
Karin (Angry Mode, Attracted Mode against Sasuke)
Suigetsu Hōzuki (Water Arm Mode)
Jūgo (Curse Mark Mode)
Pain (God Mode)
Konan (Angel Mode)
Yugito Nii (Reincarnated, Matatabi)
Yagura (Reincarnated, Isobu)
Rōshi (Reincarnated, Son Gokū)
Han (Reincarnated, Kokuō)
Utakata (Reincarnated, Saiken)
Fū (Reincarnated, Chōmei)
Hanzō (Reincarnated)
Deidara (Reincarnated)
Sasori (Reincarnated)
Hidan (Jashin Ritual Mode)
Kakuzu (Shinzo Mode)
Asuma Sarutobi (Reincarnated)
Nagato (Reincarnated)
Second Mizukage (Reincarnated)
Mū (Reincarnated)
Third Raikage (Reincarnated)
Fourth Kazekage (Reincarnated)
Madara Uchiha (Reincarnated) (Rinnegan Mode)
Haku (Reincarnated) (Ice Mode)
Zabuza Momochi (Reincarnated) (Demon Mode)
Chiyo (Reincarnated) (Chikamatsu Ten Puppets Mode)