I've played parts of Sands of Time, I own Warrior Within (beat twice), and beat Two Thrones at my friend's house.

I personally think Warrior Within but Two Thrones is EXTREMELY close! Warrior Within was just a lot more fun to play with the dahaka chases and the plot seemed more gripping for some reason don't ask why. Therefore, my vote is Warrior Within.

Only thing I think two thrones has over Warrior Within is the bosses and the dark prince character is fun as a character and to play as (except for the draining life).

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