During the intro, the Empress will recount the events of the last game, and how they lead to this one. During her narration, she will say "Some believe when the Prince journeyed to the Island of Time to escape death, he returned alone, the amulet destroyed, the Dahaka appeased, the Empress dead. The Prince was free at last. But, this is not how it happened." This line is actually a reference to the bad ending of the previous game, Prince of Persia: The Warrior Within, in which those events occur.

The last lines of dialog the Prince says are supposed to be the same as what he says in the first game, The Sands of Time, meaning he was telling the story of all three games to Spoiler:Farah after they defeated the Dark Prince and Zurvan. However, the last lines the prince says were changed. In the Sands of Time, his last lines were, "...You may wonder who I am or why I say this. Sit down and I will tell you a tale like none that you have ever heard..." In the Two Thrones, he says, "...You may wonder who I really am or why I say this. Come, and I will tell you a tale like none that you have ever heard..."

The Two Thrones started out as "The Kindred Blades". It had the same dark tone as Warrior Within, a different model for the dark prince, and some changes to the story (Spoiler:such as Kaileena unleashing the Sands of Time by killing herself in order to save the Prince, instead of being killed by the Vizier for him to gain god-like powers).

Zurvan, the name that the Vizier takes for himself, is the god of time for the ancient Persians. He was also a neutral god since his twin sons were the personification of good and evil. His sons were Ormazd and Ahriman, which are the deities found in Prince of Persia (2008).