The world of Rune Factory has two major civilizations: the steampunk Sechs Empire and the magic Kingdom of Norad. For centuries the Empire has sought to destroy the Kingdom, but the war has always remained a stalemate. Eventually the Empire discovers the existence of Four Dragon Gods who created the RF world: Terrable of Earth, Fiersome of Fire, Aquaticus of Water, and Ventuswill of Wind. The Empire awakened and tried to enslave the Dragon Gods in hopes they can be used as a secret weapon. Like all evil empire plans, it’s a total failure, and only results in making the Dragon Gods very pissed at all mortals.
The player always controls a powerful warrior-mage (turned farmer) who suffers from amnesia. These warrior-mages (turned farmers) are mysteriously being summoned from various locations, but no one knows who is doing it. The warrior-mages (turned farmers) have been opposing the Sechs Empire and Dragon Gods from destroying Norad.
RF1 and RF Frontier features Hero #1, who defeats Terrable.
RF2 features Hero #2 and his child. The two join forces to defeat Fiersome.
RF3 features Hero #3, who defeats Aquaticus. Hero #3 is a werebeast (half-human/half-monster), and helps bring the two races together.
RF Tides of Destiny features Hero #4. This hero does not fight a dragon, but instead a mysterious entity. The entity tries to use the repeating warrior-mage summoning for his own plans.
RF4 is going to feature Hero #5, who is facing against Ventuswill.
The plots to each individual game is simplistic. The warrior-mage shows up, meets a girl/boy who gives them a home (and farm) to live on, and befriends the local town. Near the town, monsters are threatening to take over. The warrior-mage then goes about stopping the monsters, find the hidden Dragon God, and then defeating it to save the world. Along the way, the warrior-mage regain parts of their memories.
All RF are, more or less, taking place within the same time frame (but different locations in Norad). The warrior-mages are being summoned for a purpose, but this epic reason hasn’t been revealed yet. I suppose it will be in the next title after RF4 (probably for Wii U).