On a rainy day a monster drops out of sky, knocking it unconscious. Shara discovers him and brings the monster inside her house to nurse him. A moment later the monster transforms into Micah, a human child. Not able recall any of his memories, Micah is offered the chance to live in the sacred tree located on the outskirts of town. Micah is allowed to live there as long as he can maintain the farmland within the tree. While starting his new life, Micah must find out why he has the ability to transform into a monster and keep it as a secret from everybody else at the same time.
Just like in the previous installments, Rune Factory 3 lets the player farm almost real-time. As they play the game, times passes and the player can do certain things only in daytime. As days pass by, the crops will grow according to the time that has been passed.
The player is given two bars, one for health point and another one for rune point( the game version of energy points). The rune points allows actions such as plowing or watering the farm; it also act as magic point for magic as well. When player is out of RP, player's actions depletes health points instead. When the character is out of HP, the player will be forced to return home. If the player continues to abuse the character, the character will be sick and will be forced to buy medicine to heal.
One special feature that has been added is the ability to transform the main character into a monster. However this feature does not greatly impact the gameplay, it is only used as the key concept for the story.
As part of Harvest Moon franchise, the player must farm crops, fruits and vegetables to help proceed the main story.
On the field, player must fertilizes first before planting crops. The process includes removing weeds and rocks. After so a hoe is used on the field to make sure the ground is suitable to be planted. When it come to planting, the right crops need to be planted corresponding to the weather, otherwise the crops will wither and die before producing any fruits or vegetable. Weather affects farming gameplay than just one way. For example, during summer storm will pass by the field and destroy the most of the field, forcing players to start all over again from the beginning.
Soil potency is also factored into growing time. The longer a plot of land is continuously used the longer it takes for crops to grow. To refresh the soil the player will have to use crop rotation. When crops are picked they will occasionally drop seeds for a higher level version of the same crop. Crops that can be harvested multiple times will also slowly level up over time. Higher level crops sell for more gold and make more potent meals.
Just like any RPG game, player can equip various weapons and protection gears to help fight against monsters. Weapons include long sword, short sword, hammer, axe and such. A new addition to the series are dual daggers, giving more speed than attack power. Along with weapons, the player also can use magic as well, both offensive and defensive magic. Offensive magic has various elemental and attack types.
Players can develop relationship between different female characters in the game. However only one of them is allow to be married with the main character. The player can raise the relationship by either completing the job that was posted on town's bulletin board or by giving them presents. When the relationship has reached to the max, marriage proposal item must be given to female character to start marriage.
Most townsfolk, after achieving a certain level of friendship, can be invited along into combat. They each have a weapon type they specialize with, gain XP and level along the player avatar, and can be given new weapons and accessories to equip by the player.
Shara : A kind and generous girl who raises flower with love and care.
Collette : Works at the diner.
Marian : Outgoing girl who's training to become a doctor. However her treatment don't always go as planned.
Karina : Unbelievably lazy girl who works at the general store. She's usually napping on the job.
Pia : The bathhouse assistant who is actually a mermaid.
Sofia : Has habit of speaking in opposites.
Sakuya : An inn attendant who loves to travel. Sell items she find in dungeons.
Carmen : Loves fishing. Helps out at the family fishing resort. Full of energy and easily excited.
Raven : Likes to keep to herself, and doesn't interact much with other people.
Kuruna : The proud elder of the Unvir settlement. One of the last remnants of her ancient race.
Daria : An excitable and eccentric artist of many mediums. Loves rainbows.
Player can tame wild monsters and keep them. They can be used to help farming, produce rare items, or help the player during battles. Inside the farm, player must keep the barn stocked with grass for the monsters to have them produce high quality items such as eggs and milk. Outside the farm, once assigned monsters will follow the player until they have no more HP or player send them back to farm. The main character can ride some monsters.
Player can take various jobs from town's bulletin board. Some of the jobs are repetitive missions, which can be done over and over. Other missions help raise relationship levels with villagers. However some of them are required since they not only raise relationship with love interests, but are needed to marry them.
Crops and foodstuffs purchased form the general store can be cooked into meals which replenish HP and RP and provide temporary stat boosts. After the tree expands the player can also create medicines from herbs and flowers and weapons and accessories from ore and monster drops. Weapons and accessories can also be reforged with additional materials, increasing their level and adding additional stats based on the material used in the forging.