SaGa Frontier 2 has two separate storylines: one is the history of Gustave XIII of the country of Finney, and the other concerns a character named Wil Knights. The game takes place in the land of Sandail, with the game's timeline spanning several decades.
Gustave XIII is the former prince of Thermes, the capital of Finney, and was intended to be the heir to the throne of his father, Gustave XII. The son is disinherited and exiled by his father when, at the age of 7, he fails to manifest any magical abilities, known as Anima, during a ritual known as the Firebrand Ceremony. His mother, Queen Sophie, unsuccessfully tries to prevent Gustave XIII's banishment. She and Gustave XIII are banished from the castle by Gustave XII and are forced to live in the slums of Thermes. Master Cielmer, a magician as well as teacher and councilor to Gustave XIII assists both mother and son in escaping Thermes and seeking asylum in the city Gruegel in the kingdom of Na. Despite being granted a mansion to live in by the king of Na, Gustave is still resentful of his rejection and lack of magical powers.
At age seventeen he apprentices as a blacksmith and learns to fight, and it is during his period his mother dies. He then moved to the city-state of Wide where he insinuates himself with the ruler and overthrows him. Five years later, Gustaves father dies, and at the behest of his best friend Kelvin decides to claim the throne. A war then breaks out between Gustave XIII and his half-brother in which Gustave conquers Finney and becomes the ruler of all the surrounding kingdoms except Na. This one holdout is controlled by Phillip, Gustave's brother, who blames Gustave for their mother's death. During the subsequent conflict, Gustave admits he lacks magical powers, and abdicates in favor of Phillip. Gustave then builds a city of his own called Hahn Nova, but it is overrun by monsters and burned to the ground. The fate of Gustave and his friends is left a mystery.
The secondary playable storyline in the game is that of Wil Knights, who is a member of a rich family of "diggers"; after the death of his parents, Wil relocated to the kingdom of Westia. At the age of fifteen Wil sets out to become a famous digger: after hearing about a legendary object known as "The Egg", Wil sets out to find it. After adventures in the Arctic region of Weissland, Wil becomes known as "Tycoon Wil", though he continues to search for the Egg. Wil then has a son named Rich who goes in search of the Egg and finds a young woman named Misty in possession of it. And even though his wife announces their baby girl Ginny has been born, he becomes obsessed with the woman and the Egg, and never returns from his quest.
The final part of the story involves Ginny Knights following the path of her father and grandfather in searching for the legendary object. Upon hearing of the evil powers of the Egg, and its role in leading her father to his death, Ginny decides to find and destroy the object. She eventually discovers the Egg is now possessed by "Fake Gustave", a pretender to the throne of Finney trying to take power in the wake of Gustave XII's death.
