The game takes place a year after Tales of Xillia. Under orders from her father to find the mystical Land of Canaan, Elle Mel Marta boards a train which is hijacked before its departure. Ludger Will Kresnik follows her onboard and works with Jude Mathis to retake the train. The train crashes and the resulting medical treatment from Spirius Corporation puts Ludger in debt. Aware of the Kresnik family's ability to destroy parallel dimensions, Spirius CEO, Bisley Karscy Bakur, hires Ludger for this purpose since the spirit Origin can no longer sustain the abundance of souls in the worlds. At the same time, Ludger searches for his brother, Julius Will Kresnik, who has been declared the train hijacking's instigator.
The game will also introduce a new choice system into the game, where players are allowed to choose between two courses of action in the game by pressing the "L1" or "R1" buttons on the controller. The effects of these choices can range greatly from simply different dialogue during a cutscene or choosing between fighting an enemy or retreating. The game will also utilize the XDR-LMBS or Cross Double Raid Linear Motion Battle System for its combat, which is a variant of Xillia's Dual Raid Linear Motion Battle System. Party members will have special abilities in battle, such as Ludger's Weapon Shift, where he can swap between swords, guns and a hammer during combat.