The Sultan of Persia and his son-in-law are visiting the Sultan's brother, Assan. The friendly family meeting soon turns into a nightmare: Assan kills the young Prince's bodyguards, locks him up in a prison, and captures the Sultan. The reason is a little disagreement between the brothers regarding matrimonial arrangements: it appears that the Sultan had promised his daughter to Assan's son, Rugnor, and later broke his promise by letting her marry the Prince. In the resulting turmoil, the Sultan is killed, and the Princess is kidnapped by Rugnor, a ruthless half-tiger creature. The Prince must figure out a way to find Rugnor, defeat him, and rescue his wife.

Prince of Persia 3D is just what its title implies: an action platformer with puzzle-solving elements in the style of the previous Prince of Persia games, but set in a three-dimensional environment. The Prince still has to time his jumps, avoid deadly traps, interact with the environment, and fight Rugnor's minions who will try to stop him.