Set seven years after the events of Prince of Persia: The Sands of Time, the Prince finds himself constantly hunted by a terrible beast known as the Dahaka. The Prince seeks counsel from an old wise man who explains that whoever releases The Sands of Time must die. Because the Prince escaped his fate, it is the Dahaka's mission as guardian of the Timeline to ensure that he dies as he was meant to. The old man also tells of the Island of Time, where the Empress of Time first created the Sands. The Prince sets sail for the Island in an attempt to prevent the Sands from ever being created, an act he believes will appease the Dahaka. After a battle at sea with an enemy force led by a mysterious woman in black capsizes the Prince's ship, the Prince washes ashore unconsciously onto the Island of Time.
He later awakens and chases the woman in black through the Empress of Time's fortress into a portal that transports the two into the past. The Prince saves a woman named Kaileena from being killed by the woman in black, whose name is Shahdee. Unable to grant the Prince an audience with the Empress of Time, who is busy preparing to create the Sands, Kaileena instead tells him how to unlock the door to the throne room in which the Empress resides. The Prince makes his way through the fortress, utilizing the sand portals to travel back and forth between the past and present, and narrowly escapes several encounters with the Dahaka, who he discovers cannot pass through water. The Prince activates the mechanisms in the two towers of the fortress - the Garden Tower and the Mechanical Tower - that serve as locks to the door. He returns to the throne room only to discover that Kaileena is actually the Empress of Time herself, who has foreseen in the Timeline that the Prince will kill her and who has decided to attempt to defy her fate, just as the Prince is doing. A battle ensues and the Prince proves victorious; he kills Kaileena and returns to the present. What lies ahead is the most dramatic Twist in the Prince's life, and He starts believing the priest who told him "You cant change your Fate! No Man Can.." But Prince is not going to give up that easily.