TALES OF XILLIA 2 focuses on the events a year after the climactic end of TALES OF XILLIA. Players assume the role of Ludger Kresnik, a young man with a zest of cooking who lives with his older brother and his cat, named Rollo. On his way to his first day at work for a local cafeteria he runs into a young girl named Elle Marta and the two soon become involved in an accident that will change both of their lives forever.

TALES OF XILLIA 2 focuses its story theme around the concept of "choice", which is also expressed heavily in the game's overall gameplay mechanics. Throughout Ludger's journey the player will be able to decide how he reacts to various characters and situations. These choices can cause the story to branch out into different paths depending on the player's decisions.