The Two Thrones follows the second ending of Warrior Within, in which the Prince kills the Dahaka and successfully alters Kaileena's (The Empress of Time) fate. While on a ship on route to his home city of Babylon, the Prince tosses his magical medallion overboard, as he believes he no longer needs it. He has promised Kaileena that no harm will come to her in Babylon, but upon returning, he is horrified to find the city is burning and ravaged by war. His ship is attacked and he and Kaileena are thrown overboard. Kaileena is taken prisoner after drifting ashore.
After fighting his way through the city, the Prince discovers that as a result of his efforts on the Island of Time to prevent the Sands of Time from being created, the events of the original games never happened- the Vizier was never killed. Worse, he now possesses the empty hourglass, the Dagger of Time, and the magical staff. The Vizier is now in search of the Sands of Time, and has captured the Empress of Time to get them. Just as the Prince finds Kaileena, the Vizier kills her, and unleashes the Sands of Time, which strike and mutate the Vizier's lieutenants into hideous sand monsters. Then, by impaling himself with the dagger, the Vizier transforms into a monstrous, immortal winged demon. The Prince is also struck by the Sands of Time, although the effects on him are not revealed until later in the story. The unleashed Sands of Time cause the palace to fall apart and collapse. The Prince falls as the floors collapse around him, but not before stealing the Dagger of Time.
Later, the Prince finds that the Sands of Time have split him into two personalities: his usual self, which although flawed strives to be good and noble; and the "Dark Prince" who represents the more cruel, avaricious, and arrogant aspects of his psyche, and is manifested as a bitter and cynical inner voice. Whenever the Dark Prince is dominant - in the absence of water, and when he is able to feed on the Prince's fear and anger - the Prince assumes his dark, corrupted form, although his mind remains intact. In his natural state, the corruption of the Sands is limited to a glowing wound on his left arm and shoulder, where the Sands had fused a razor-sharp chain weapon known as the "Daggertail" into his flesh.
Meanwhile, the Vizier has transformed his army (and even some of the population of Babylon) into Sand monsters. While searching for a way to defeat the Vizier, the Prince once again encounters Farah, who does not remember him, and is surprised that the Prince knows her name. Although initially wary of the Prince, she agrees to help him defeat the Vizier.
As they travel together, the Prince continues to endure the inner struggle between his compassion and the selfishness of the Dark Prince. The Prince's growing affection for Farah compels him to embrace a more selfless perspective, beginning with concern for Farah and developing into compassion for his downtrodden people. As this begins to happen, he realizes that the Dark Prince, who claims to be part of him, is in fact a Sand monster, who is vying for control of the Prince and his kingdom. A particularly heroic and selfless deed proves a turning point in his mission, as his heroism inspires a new hope in the populace. With their spirits lifted by the knowledge that their Prince is fighting to save them from the Vizier, they rise up in defiance of his army, and provide just enough of a diversion for the Prince and Farah to get through the horde of Sand warriors guarding the palace.
As they approach the throne room, they are ambushed by the Vizier. He captures Farah, planning on making her his concubine, and sends the Prince plummeting deep into a dry well, who survives only by transforming into the Dark Prince. As he goes further into the well, the Dark Prince's voice grows stronger and more hostile, fueled by the lack of water and the Prince's desperation. The Prince eventually comes across a dark room to find his father, King Sharaman, lifeless on the ground. Overcome with grief and taunted by the Dark Prince, the Prince finally recognizes his own immaturity underlying his constant efforts to undo his mistakes. He resolves never to walk down that path again, and to accept the consequences of his actions. With this resolution, he silences the Dark Prince and reverts to his natural form - without water. Taking up his father's sword he makes his way up the tower to complete his mission.
Using the Dagger of Time and his father's sword, the Prince is able to defeat the Vizier and free Farah. With the Vizier's death, his army vanishes and Kaileena's soul is freed from his grotesque form. She thanks the Prince by cleansing him of his corruption and removing the Daggertail, before leaving the world for another more suited to her presence, taking the Dagger of Time with her. However, as the Prince leans down to reach for his father's crown, he is confronted by the form of a dark warrior, as prophesied at the end of Warrior Within. Before the Prince's eyes, the dark warrior metamorphoses into the Dark Prince, who swings his Daggertail and draws the Prince into the mental realm where the two battle for control. With some help from Farah, the Prince realizes that battling his inner demon only serves to feed it, and will trap him forever within its realm. In the end he turns away and follows Farah up an ascending staircase leading to a bright cleansing light. Starved of anger, greed, and pride, the Dark Prince is finally defeated. The Prince awakens back in the real world to Farah's warm embrace.
Veterans of The Sands of Time are then treated to a tribute and reference to the first game in the trilogy. As they look out over Babylon, Farah asks the Prince how he really knew her name. He then begins to tell her the story of the first game, using the same monologue as the introduction and ending of that game, thus bringing the trilogy full circle: "Most people think time is like a river, that flows swift and sure in one direction. But I have seen the face of time, and I can tell you, they are wrong. Time is an ocean in a storm. You may wonder who I am and why I say this. Come, and I will tell you a tale like none you have ever heard...."
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