In Rune Factory 2 the player, Kyle by default, is an amnesiac who wanders into the town of Alvarna and is discovered by a girl named Mana.
Like in the first Rune Factory game, the gameplay is a mix of the farming found in the Harvest Moon series and battling. The player must grow and maintain crops and build up their home, and there are also dungeons to battle and befriend monsters in. The stamina of your character still depends on the meter of rune points, and once it is depleted it will start draining the meter of health points.
The player will marry a potential girl in the town and have child with her, the gender of the child will be of the player's choosing. Unlike the Harvest Moon games, the player will then continue playing as the child which is an integral part of the game's plot. At the point the goal of the game is to build a school, a goal left behind by Kyle one night when he left home.