The events of SaGa Frontier take places in a fictional universe called "The Regions", which incorporates different worlds with various degrees of technological development. The player can choose to follow one of the seven available scenarios, each dedicated to a different protagonist.

The seven protagonists of the game are: a half-human, half-Mystic girl named Asellus, who is rejected by both races and will eventually have to decide where she belongs; the twin mages Blue and Rouge, who must descend into hell in order to find answers concerning their true identity; a part-time model and secret agent Emelia, who is wrongly accused of murdering her fiance; Lute, a bard who was kicked out of his house and who embarks on a quest to avenge his father's death; a teenager named Red, who becomes a superhero in order to bring down an evil syndicate; a Lummox (a race of fox-like creatures) named Riki, whose entire world is in peril; and finally, T260G, an ancient robot who awakens in modern times and needs the help of a human to survive.

SaGa Frontier plays similarly to its immediate predecessors in the series; utilizing the so-called Free Scenario System, the game allows non-linear exploration and features many side-quests, atypically of Japanese RPGs. The battles, however, are handled similarly to most representatives of the genre: using physical attacks, special skills, or magic, the player-controlled party engages the enemies in a turn-based fashion. There are no random battles in the game; all the enemies are visibly walking on the field.