Taking place one year after the events in Xenosaga II, this final release in the futuristic, Nietzsche-inspired RPG trilogy follows protagonist Shion as she joins an underground movement to investigate the nefarious deeds of Vector Industries. The turn-based battle system borrows elements from the two previous installments and adds a "break system" for another layer of strategy. Characters all have a break gauge that fills with each enemy attack; when the gauge is full, the victim will be unable to act for two turns.

The cinematic storyline is brought to life with more than eight hours of cut-scenes and voice-over dialogue. Character customization is enhanced with a branching skill system, and players are able to purchase, barter, or sell any items and equipment they encounter during the adventure. Progress within the universe is tracked using the in-game database, which records major events, people, items, locations, weapons, and more. New puzzle mini-games are also available for a change of pace, offering 60 levels of brain-teasing action and a map editor for custom challenges. ~ Scott Alan Marriott, All Game Guide