The player takes on the role of Maia, Queen of Halassar, who is the goddess Laharah reborn, and can transform herself into a variety of "summonable" creatures. The game's story revolves around Maia's quest to heal the World Tree, Eleh, which was shattered by the Storm.

The game takes place 20 years after the previous. Halassar, a province in the Empire of Galdyr, distant from the kingdoms of Medeva and Orenia, was foretold as the birthplace of the Goddess Laharah Reborn. The priestesses of Laharah declared Maia as the goddess when she was an infant and armies rose up in Maia's name, led by the Emperor's brother Prince Taurgis, making Halassar independent from Galdyr and Maia, the Queen of the Halassar Empire. Traveling with her is Sangaril, an orphan trained by the Shadow Clan assassins of the Munari, who was sent to kill Maia as a child, but instead became her sworn bodyguard. While reclaiming the Book of Prophets from the Halassar Palace traitor Dama Sivora, Maia activates a rune stone embedded in the pirate island stronghold of Prince Neru, on the Isle of Teomura, gaining the ability to transform into one of the 4 Summons. After recovering the Book of the Prophets and returning to the Palace she learns more about her destiny.