The antagonists of the previous game, Saturos and Menardi, have been slain in battle by the game's protagonists led by Isaac[19], but not before the pair succeeded in activating two of four great lighthouses situated across the world of Weyard, the Elemental Lighthouses.[20] But now Saturos' remaining travelling companion, Felix, has taken the rest of Saturos' group and now sets out on a journey of his own to complete Saturos' original objective to activate the remaining two Lighthouses, for lighting all four will achieve the restoration of the powerful force of Alchemy to Weyard.[20] Sailing the oceans of Weyard on a ship with their new companion Piers, Felix and his party embark on an epic expedition while pursued by Isaac's party.[21]
Eventually, Felix's party is able to achieve entrance into a legendary, secluded Atlantis-like society named Lemuria far out in the ocean.[22] When they convene with Lemuria's ancient king, Hydros, they learn about Alchemy's true nature; it has always been the sustenance of Weyard's very life force, and its absence over the past ages has caused the world's continents to decrease in size and parts of the world to collapse into the abyss.[23] Knowing that restoring Alchemy is what must be done to actually save the world, Felix sets out to climb and activate Jupiter Lighthouse. But when Isaac's pursuing party enters the lighthouse, they are trapped and ambushed by the vengeful Mars Adept Warriors, Karst and Agatio. Felix comes to assist Isaac to defeat Karst and Agatio.[24]
Felix is finally able to explain to Isaac why Alchemy's release is a necessary thing for everyone, and that Saturos and Menardi were aiming for this goal merely for the sake of the survival of their home colony of Prox to the far north, located near the Mars Lighthouse.[25] Felix and Isaac's two traveling parties join forces to form one unified group that sets out north to activate Mars Lighthouse[26]; however, when they reach the tower's top, the Wise One, the entity responsible for originally tasking Isaac to prevent the breaking of Alchemy's seal, confronts them. He warns them that mankind could very well destroy Weyard themselves if they had possession of such a power[27], and when Isaac insists on breaking the seal regardless the Wise One summons a giant, three-headed dragon for the party to battle in the final struggle.[28]
When the party of Adepts have slain the dragon, they discover that the Wise One had transformed Isaac's father and Felix's parents into the now-dead beast."[29] After a short period of mourning, they gather the resolve to finish their objective and activate Mars Lighthouse; with all four towers across Weyard lit, the process that heralds the return of the force of Alchemy to Weyard ensues at the mountain sanctum Mt. Aleph. Alex is there, however; he took advantage of everyone else's quests so that he would gain immense magic power for himself when Alchemy is unleashed.[30] Unfortunately for him, though, the mountain collapses and sinks into the ground with him still on it.[31] The Adepts, in the meantime, find that their parents have actually been revived by Alchemy's return[32], just as the Wise One originally planned.[33] They are able to recognize that the reason the Wise One appeared to play that cruel trick on them before was to test their resolve as Adepts, and therefore test their ability to handle a great new responsibility: To ensure that throughout the world the newly released force of Alchemy is not abused by Weyard's populace like it was in the ancient past.[33] The game ends as the Adepts and their parents return to their hometown of Vale to find that it has been destroyed by the energy let loose by the breaking of Alchemy's seal, but that their families and the other townspeople have survived because the Wise One warned them of the impending danger in advance.