The story follows Kyle Dunamis, a young boy with dreams of becoming a great hero like his father Stahn, the hero of the first game. When Kyle sets off one day to the local ruins with his adopted brother Loni, hoping to land an enormous lens that will help to fund his mother Rutee's orphanage, he crosses paths with Reala, a mysterious girl who claims to be searching for a hero. Kyle's determination to prove himself the very same hero that Reala is searching for leads him into conflict with the seemingly benevolent Fortuna Sect, and sends him on a wild journey across time that brings him into contact with many prominent figures from the first game.

The skits that the series is now well known for make a return as well, with characters represented in these sequences by full body portraits for the first time in the series. These portraits, along with the rest of the game's character art, are handled by Mutsumi Inomata, returning to the series after her work on Destiny and Eternia. Inomata's distinctive style, easily identifiable by her character's long, slender limbs and unconventional fashion, is not to all tastes, but several of the game's characters have enjoyed enduring popularity among series fans, ranking within official listings of the series' most popular characters, and making appearances across other media.