This game is the fourth installment of the main series. The game is the first to be presented in 3D, both in environment and in combat.

The story starts with an orphaned girl from the late Zhao state, Shui Jing (水鏡) and her senior disciple-sister, Qu Xian (屈嫻) on the top of a mountain with their seniors from the House of Mo, a Mohist clan actively opposing the tyranny of Qin and its leader, who is often accompanied by a mysterious purple-skinned adviser (later revealed to be the original Vessel Spirit on an ideological mission to create an unified utopia by absorbing the mortal world into the universe created by the Spirit - "Realm in the Clouds"). Qu Xian witnessed her companions being murdered by giant mechanical constructs created with the Jiguan technique. Later, Shui Jing meets with Ji Liang (姬良) (later known as Zhang Liang 張良), a well-educated young man from the annihilated Han state who can utilize the Scroll of Heaven (Tian Shu 天書) in battles after obtaining and deciphering it in an early escapade with Shui Jing, and Ji Peng (疾鵬), a humorous talking bird king who employs a humanoid Jiguan body in battle. The three journey across various lands to combat the machinations of the Qin Empire and the Vessel Spirit. Later in the story, Ji Peng is revealed to be the bird owned by the Mo clan leader's husband, Fu Ziche (輔子徹) (introduced in Dance of Maple along with the current Mo leader, Lady Wenjin (紋錦), renowned for her eternal youthfulness), who had been sealed in ice in the World Within the Vessel after a battle with the Vessel Spirit during which he averted disaster by preventing the Black Fire the Vessel Spirit unleashed using a purple crystal in desperation from taking form. The trio eventually reconcile their differences with the Spirit, rescued Fu Ziche, and confronted the true threat, battling with all nine portions of Black Fire (with each portion increasing its power and all nine portions 4^128 times as powerful as one portion alone) running amok, which is believed to be the ultimate weapon of the Hell that can take the form of a black dragon, discovered long ago using purple crystals by the ancient Shu kingdom engineer Qi, who caused the destruction of his civilization and was sealed away in a protective cocoon until the events of the game, when he took control of Lady Wenjin (who was created with Black Fire) and Black Fire to go on a rampage to destroy the world (or in his mind, creating a world where hell and the mortal realm co-existed in order to eliminate death) upon awakening.