Rune Factory 2 takes place years after the happenings of Rune Factory: A Fantasy Harvest Moon. In this game you start out as Kyle and as you play you meet many new villagers and even get married. Some of the villagers are related to or may mention previous Rune Factory characters. However, none of the previous characters will make an appearance, except for one person, Cecilia.
As you progress through the game you explore four unique areas, battle monsters, get married, make friends, plant crops, and much, much more. After a certain point, Kyle leaves and you play as his son or daughter, depending on which gender you choose for the child. You then play as the child in the same manner as Kyle. You cannot get married, but you do have the option of getting a girlfriend or boyfriend depending on the gender of the child you choose.
But no matter what, Rune Factory 2, like its predecessor, proves be a spin off of the normal peaceful Harvest Moon game. A great game for people that love Harvest Moon and just want a little more adventure and action in the game.
 Storyline - First Generation
Warning! Spoilers ahead.
Kyle has just arrived in Alvarna with no memory of who he is or how he got there. A girl named Mana and her father Douglas find him and give him a farm that they own. Of course, not all is peaceful in this town as it has been recently troubled with mysterious earthquakes. Kyle must find out why the earthquakes are happening and how to stop them while starting a new life.
Eventually, Kyle marries one of the bachelorettes in Alvarna and has a child (the gender is up to you). When the child is born, Kyle and his wife arrange for a school to be built so that their child can have an education.
 Storyline - Second Generation
Warning! Spoilers ahead.
On a stormy night, Kyle suddenly remembers who he is and why he has come to Alvarna. He leaves suddenly, giving an ancient manuscript written in Earthscript to his child. Therefore, it is up to the child to unravel the mystery surrounding his or her father's disappearance. With the help of Barrett, who is now working at the school, he or she deciphers tablets found in the monster-infested mountains and forests, and eventually figures out why Kyle left: a great monster named Fiersome, bound by magic for 1000 years, is beginning to break free due to time running out on the seal.
The child discovers the Fiersome is bound deep under the city (the earthquakes were from its struggles to get out), and he or she journeys down to reseal it, armed with a powerful spell called Dragon Break. Although the spell is successful, Kyle has sealed himself within Fiersome and cannot return home since he is forced to return to the Forest of Beginnings.
Upset, the child heads home, but then discovers that there are new areas to explore in the four seasonal areas he or she had just gone through. A new tablet is discovered, which yields the spell Omni-Gate. The child uses this spell and Kyle is able to come home again to his family and friends.
- Fight, befriend, and work with monsters, including some new ones and some old ones from the last Rune Factory.
- Play as both Kyle and Kyle's son/daughter, in the same game.
- Court several bachelorettes for the first generation of the game, and boyfriends or girlfriends for the second generation.
- Many villagers live in Alvarna, and all have their own likes, dislikes, thoughts and dreams.