The Prince starts this journey staring at his reflection in the medallion, the very medallion that had protected him for seven years. He no longer wanted anymore fighting nor perils, ahead was home and nothing but glorious rest and peace to look forward too with his beautiful companion, Kaileena. Sailing swift and sure to Babylon, his comfortable home was nearly in sight, his newly found freedom allowed him to drop the medallion overboard. But the metaphorical ocean of time was disturbed and the ripple he had created traveled further then even the Prince could foresee...
His sails unfurled in the light wind and the bow of his makeshift boat pitched gracefully over the soft waves that rolled into Babylon's port. Sailing between the massive cliffs that protected his city from the open sea, the stones as old as the world marked the entrance to his home. Babylon and its signature tower appeared before him, but something was wrong. Shock grew to panic when his small vessel was met not by cheers and the embrace of family, but by fire and arrows. The walls of his homeland had seemingly stretched up against him, vicious and foreign. He was not safe, nor was Kaileena beside him.
He came home seeking comfort and found only war, but war with who? Making his way through the palace, he learns that his enemies' leader is none other than the evil Vizier that he thought was long dead. Not realizing that because of his meddling with the timeline, the events of The Sands of Time never happened. The Vizier had never perished at the Prince's hand and he still had his reckless ambitions of immortality. Dagger of Time in hand, the Vizier murdered Kaileena in front of the Prince (who was incapacitated by one of teh Vizier's minions, wielding a daggertail whip embedded in the Prince's arm) and unleashed the Sands of Time once more. The promise of power fulfilled, he stabbed himself, gaining immortality and transforming into a strange new monstrosity. The sands did as they had before, sweeping across the palace and infecting all in their wake. As the terrace began to collapse, the Prince recovered the dagger and started the slow trek back towards the palace.
Unfortunately for the Prince, he too was tainted by the sands, giving rise to a corrupted charred version of himself, the Dark Prince. Along the way, he battles the Vizier's army, all tainted by the sands. Along the way, he learns that while in extreme states of emotion, he will trasform into the Dark Prince, and gain the ability to use the daggertail whip in his arm, and that he can revert to his normal state if he touches water. The Prince also encounters Princess Farah, whose homeland was also destroyed by the Vizier. However, the Prince soon realizes that Farah remembers nothing of their past together and he has to resort to merely claiming to have heard stories of her beauty (and hastily amending with her bravery as well). With his unlikely partner in tow, they both journey to put an end to the madness. However, conflicts increasingly arise between the unforgiving vengeance and ruthless violence of the Dark Prince and the more compassionate Farah.
As they enter the palace however, the Vizier captures Farah and casts the Prince into the palace's well system (now drained and totally dry). After being in the Dark Prince form for an extended period of time, the Prince finds his father's body. Finally, he realizes the truth: he has been childishly running from conflict all this time, instead of dealing with his troubles like a man. Coming to grips with this, the Prince takes up his father's sword, which illuminates in the darkness, and with his realisation of his mistakes, is able to force himself to revert to his usual form, while at the same time conquering the Dark Prince's influence over his mind, and goes to save Farah. After a long fight, the Prince manages to destroy the Vizier with the Dagger of Time. As he goes to recover his father's crown, however, the Prince sees the Dark Prince before him. What follows is a battle in the Prince's mind between himself and the Dark Prince. The fight drags on until Farah urges the Prince to let go of his anger. He leaves, destroying the Dark Prince forever and returning to the waking world. As they look out over Babylon, Farah asks the Prince how he really knew her name; he responds by telling her the story from the very beginning...