Rune Factory 2 is set several years after the first game. The evil Sechs Empire has been defeated, and the Kingdom of Norad is once again at peace. Things may not stay that way for long, however, as dark premonitions foretell of dangers to come. It's up to player to uncover the source of these premonitions and bring peace to the kingdom once more.

In a first for the Rune Factory series, the story of Rune Factory 2 is multigenerational. Players begin the game as Kyle, a strange man who comes to Alvarna Village. Eventually, players will take on the role of Kyle's child, opening up a whole new adventure.