The story unfolds via amazingly detailed cut-scenes that bring the enthralling and complex characters, powerful battle sequences and unique gameplay to life. Shadow Hearts: Covenant also brings back the innovative combat system, the Judgment Ring, which not only allows players to choose which characters to bring to battle, but also determines the final outcome of the battle based on the players' speed and accuracy. New to the Shadow Hearts sequel, are enhancements to the Judgment Ring allowing offensive team-based combos and defensive formations.

Set during World War I in a fantastical world of magic and creatures, the game takes place over a year after the original Shadow Hearts ended. Yuri, the main character is back, and he embarks on a new expedition with friends Gepetto and Kallen, a German female soldier. Yuri's morphing abilities have been weakened because he has been cursed by Nicholas, a member of a secret cult taking advantage of the war to fulfill their evil ambitions of ruling the world. Yuri and his companions must journey to find a cure for his curse and defeat the malevolent cult.