Source plot synopsis — includes the ending
As the Prince and Kaileena return to the city of Babylon, they find it ravaged by war. Their ship is attacked and destroyed, and they wash ashore. The Prince awakens and watches as enemy soldiers take Kaileena away. The Prince fights his way into the palace and confronts the Vizier, who kills Kaileena with the Dagger of Time, unleashing the Sands again. The Vizier then impales himself with it and makes himself immortal. The Prince is also affected, having a whip-like weapon known as a Daggertail embedded in his skin when the Sands infect the wound. However, in the confusion following the release of the Sands, the Vizier throws the Dagger aside and the Prince manages to steal it before the Sands infect him completely.
The Prince falls into the sewers and gets carried to the outskirts of Babylon. As he travels through the city once again to kill the Vizier, he finds that the infection caused by the Sands of Time is affecting his mind, giving rise to an alter ego called the Dark Prince, manifested by a voice within. The Dark Prince is cold, cruel, arrogant and sarcastic; he attempts to convince the Prince that he should strive to serve only himself, using his vengeance as a catalyst for his other emotions. On many occasions, the Dark Prince seizes control of the Prince's body and the Prince is fully transformed into a hybrid sand monster with abilities that allow the Prince to pass otherwise insurmountable obstacles. The Prince makes efforts to keep his transformation a secret to everyone, most evident when he is forced to flee into the sewers when he begins to transform shortly after people witness his victory over the hulking Klompa, a general of the Vizier, at the arena where they were imprisoned.
Later, the Prince encounters Farah, who is surprised that the Prince knows her name. Despite this, the pair begin to grow an entirely new romance together, but it does not hold after the Dark Prince's influence causes Farah to question his character. After Farah sets out to rescue women at a brothel and the Prince briefly parts to defeat Mahasti, another trusted general of the Vizier, Farah ends up discovering the Prince transformed into Dark Prince not long after he kills Mahasti, and her distrust of him comes to a head. She tries to stay away from him and the Prince continues into the city alone.
Realizing the negative impact the Dark Prince's corruption is having on his relationship with Farah, the Prince resolves to change his attitude and begins to ignore the Dark Prince. He resolves to fight against the suffering of his people, which the Dark Prince had always spoken against. With the occasional help of the Dark Prince's powers, the Prince gets to the royal workshop and uses a statue of his father to smash a way out for people trapped in a fire, including the old man in Warrior Within, who now expresses hope that the Prince can save his empire after initially doubting his ability to change fate. The Prince then chases and fights two more of the Vizier's generals, the Twin Warriors who are armed with a sword and an axe respectively. The Prince kills the sword-wielding Twin Warrior while Farah returns to finish off the axe-wielding one. They are then cornered by the Vizier's sand army, but are saved by the rescued citizens of Babylon, mobilizing an unexpected army. They cut an opening through the enemy forces to help the two heroes escape.
They eventually reunite at the palace entrance, where the Prince apologizes to Farah for his past arrogant and reckless attitude under the Dark Prince's influence. The Prince then repairs an elevator to bring the two to the palace's hanging gardens. Deeper into the gardens, the Vizier captures Farah and casts the Prince into an ancient well, where the long silent Dark Prince emerges once again and tries to take permanent control. The Prince resists the power, driving slowly deeper into the well looking for an escape, but he slowly weakens. At the bottom of the well, the Prince stumbles upon the dead body of his father Sharaman. He mourns for him, picking up his father's sword and accepting the consequences of what he has done to finally suppress the Dark Prince's ability to control his body. With a new resolve to set things right, the Prince fights his way underground and back into the palace halls, before ascending its massive tower to finally face the Vizier and free Farah.
At the top of the palace's tower, the Prince confronts and kills the Vizier with the Dagger of Time. The Sands are released from the Vizier and his soldiers, who die. Seeing this, the people of Babylon rejoice. The Sands take the shape of Kaileena who cures the Prince's infection and destroys the Dagger of Time. She tells him that this world was not meant for her but there will be other worlds for her where she will find her place. She also tells the Prince that his journey is at an end and then disappears. As the Prince finds Sharaman's crown, the Dark Prince takes it and tells him that whatever the Prince owns will be rightfully his and lures the Prince into his mind, where the two struggle until the Prince abandons his shadow with the help of Farah's voice. The unconscious Prince is woken up by Farah. The game ends with her asking how the Prince knows her name and the Prince answers by beginning to retell a story about his first experience with the Sands of Time in Prince of Persia: The Sands of Time.
Sources and content license
Source and revision history ↗ · Adapted from Wikipedia contributors, Prince of Persia: The Two Thrones. Section headings and formatting adjusted. · Content license