Prince of Persia 3D starts with a belly dance: the Prince and his father-in-law have been invited by Assan, the brother of the Prince's father-in-law. The dance ends with the belly dancer killing the Prince's personal bodyguards and the Prince himself being imprisoned in Assan's dungeons. Apparently, the Princess' father, the Sultan, had promised long ago that the Princess would be given away in marriage to Assan's son, Rugnor.

Rugnor is an interesting creature: half man and half tiger, he is ruthless, cruel to the teeth and covets the Princess. He is also very powerful and a master Swordsman as well. The Prince has to escape from the dungeons and chase Rugnor, as he carries the Princess away. The Prince has to fight his way through several levels including the unique Dirigible levels. The game is also unique in the Prince of Persia series, in that the Prince has a choice of 4 weapons: the Sword, a long Staff for long-range combat, Double Blades for close combat and the Bow and Arrow (with various magical arrows).