After the negative reaction to Warrior Within, Ubisoft decided to combine the atmosphere from Sands of Time with the new combat system (from WW) in order to achieve perfection. Although in theory this sounded like a great game it came out to be a huge failure (only my opinion). This is how The Two Thrones was born in 2005, considered by many fans the greatest PoP ever.
I know that your probably thinking "Why do you say it's a failure?", well let me tell you: it looks uglier than Sands of Time and the gameplay is just horrible. The perfect combat system from Warrior Within was now transformed into a buggy, glitchy, horrible mechanism and combined with the boring combat music made it look dull and uninteresting. In PoP 1 and PoP 2 the environments were great and interesting but in The Two Thrones the graphics were simple (and bad for 2005), creating a boring place with lack of imagination. Also the game's gore was almost completely removed making the finishing moves look silly. For example instead of the enemy getting cut in half he would do a back flip (I know it has no sense but that is the truth). This problems are caused by the lack of imagination and serious work from the Ubisoft programming team. They wanted to make the game fast so they ruined what could have become a masterpiece.
Although the game has its issues it also has some good parts. Prince of Persia: The Two Thrones is the first (and only) PoP that has a stealth system. It may be simple but it makes the game a bit fun in some situations. The stealth system was not the only new thing... Ubisoft also improved the boss fights making them really intense and challenging not repetitive and easy like SoT and WW.
The Two Thrones continues the story from WW and combines it with Prince of Persia: Sands of Time. After returning from the Island of Time with Kaileena (the Empress of Time) you find your Kingdom burning and invaded by the evil Vizier who manages to transform into some sort of hairless sand creature by killing the Empress of Time with the Dagger of Time (I know it sounds strange). During the transformation you manage to get the dagger back but you also get infected with the Sands of Time. Now you are a prince and a sand monster at a same time, making the game a bit more interesting. The Prince now has the ability to transform into a blood-thirsty creature that feeds on the sand of the fallen, replenishing his own life. The only disadvantages is that the transformations are scripted and only happen in specific places and while transformed your hp bar decreases. In order to refill it you must strike down your foes using new combat moves and more powerful skills. Surrounded, with nothing to loose, the Prince fights back trying to recover his throne by defeating the hairless Vizier.
Prince of Persia: The Two Thrones could have been the best PoP ever but the boring atmosphere, dull combat, simple storyline, simple environments and simple graphics transformed the game into a failure, loved mostly by people who don't know much about video games and do not accept the reality.