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- Charlotte Christine Colde: A female fencer from France, she's strong-willed and absolutely fearless with a weapon in hand. She roams the French countryside to investigate a series of calamities and put her abilities to the test. In spite of her noble background, she's most at home among the peasants.
- Earthquake: This villain is a viciously brutal American ninja standing over 3 meters tall. Availing himself of the pandemonium caused by the rash of calamities, he travels the world to rid it of its riches.
- Galford D. Weller: Bright and cheerful, Galford's the vibrant, good-guy American accompanied by his beloved dog Poppy(Female) striving to become a ninja master. Incidentally, Pahpa, Pippy, and Pippa are the female puppies who shadow Poppy.
- Gen-An Shiranui: A warrior of the Shiranui Clan, this grotesque, crafty, and foul being is feared even by his friends. He has succumbed to his devils and fathered two spawn (a daughter, Zakuro, and son, Mukuro) who battle for dominance of the Evil Path.
- Hanzo Hattori: The mightiest of the Iga ninja is incomparably cold hearted and unsparingly self-critical, spending his days in rigorous training. He takes arms against the evil proselytizer to pry his son's body and soul from Amakusa's possession.
- Haohmaru: This plain-speaking and passionate warrior wanders the world seeking mighty adversaries to perfect his own style of swordplay. He's a samurai celebrity, who also enjoys fine rice wine.
- Jubei Yagyu: Master of the Modified Shadow Style of Yagyu, Jubei treasures Bushido more than life itself and accepts his calling: leading a harsh life of wandering to perfect his technique.
- Kyoshiro Senryo: This kabuki actor, a merry fop he, likes to be noticed and put on a good show. He duels to spread the magic of kabuki to the masses and convince them of the merits of his art.
- Nakoruru: Nakoruru, said to be her tribe's greatest warrior can also communicate with nature. Foreseeing a threat to the environment, she sets out to unroot the cause of the calamities with her trusty falcon, Mamahaha.
- Tam Tam: This mighty hero of South America hides his kind heart behind a fearful battle mask. He adores children most, but their fear of him is a constant source of distress. He now scours the world to recover his village's stolen treasure, the mysterious jewel called the "Palenke Stone."
- Ukyo Tachibana: The master duelist of the sword style of Soichi Jinmu seeks nothing but the perfect bouquet to send to Kei Odagiri, the only woman who understands Ukyo's true nature.
- Wan-Fu: A general of the Qing Dynasty, this titan has both an intellect and a craftiness that belie his looks. He strives to unify China and searches for promising recruits to achieve that end - he will go wherever a strong warrior is rumored to reside.
Boss Character (non-playable)
- Shiro Tokisada Amakusa: Slain in his battle against the shogunate, Amakusa was resurrected through the power of the dark goddess Ambrosia. At that time, he seized Shinzo Hattori in the mountains of Dewa to serve as his physical vessel.
- Cham Cham: A young, catlike girl who is the younger sister of Tam Tam.
- Genjuro Kibagami: Haohmaru's greatest rival.
- Neinhalt Sieger: A Prussian Knight who fights with a giant, gun-containing gauntlet.
- Nicotine Caffeine: An old, diminutive monk, and master of Haohmaru and Genjuro both.
- Kuroko: A hidden boss. Playable through use of a cheat code.
- Rashoujin Mizuki: The first female final boss in the series and the only boss to have assistance from an animal.
- Basara: An undead spirit seeking revenge for his own murder and that of his lover.
- Gaira Caffeine: A large, brash and overbearing monk who happens to be the nephew of Nicotine Caffeine.
- Rimururu: Nakoruru's younger sister, who wields the power of ice.
- Shizumaru Hisame: A semi-amnesiac, umbrella-wielding young boy, who was the focus of the game's story.
- Zankuro Minazuki: A giant of a man and a swordsman driven insane by his quest to perfect his skills.
- Kazuki Kazama: A member of the Kazama ninja clan specializing in fire jutsu, he deserts to rescue his younger sister, Hazuki, from Amakusa's clutches.
- Sogetsu Kazama: Older brother to Kazuki and Hazuki who uses water jutsu. Unlike Kazuki, he stays with the clan and is ordered to assassinate his brother for leaving.
Boss Characters (non-playable)