Carrying the plot on from Rune Factory: A Fantasy Harvest Moon, Raguna tells of how he was saved by Mist and how she provided him with a new life. One day, she mysteriously left without saying a word. The very next day, Raguna set out to find her. He eventually comes to Trampoli and decides to rest there. He comes to the church and meets Stella. She offers to let him rest for the night. The next day, as he is about to set out again, Mist suddenly enters to church. Raguna tells her that everyone is worried about her, but she says she can't return because "Someone is calling for [her]." She instead suggests that he should stay in Trampoli as well. Though he is reluctant, there is an abandoned farm next to her's that he can stay in. Stella asks that he come back and see her afterwards.
On the way there, Raguna spots something in the sky. Mist explains that it's Whale Island and it's always in the sky over Trampoli Village. She shows him to the farm and gives him a cheap hoe and can, and turnip seeds. She says she looks forward to eating them.
Talking to Stella once again, she requests that he take a bamboo shoot to Turner at the inn. There, Raguna meets Eunice. From there, he gives the bamboo shoot to him and is asked to talk to Ganesha about fixing his kitchen knife. There, she agrees to go over but requests that he give Danny of the General Store the payment for her tab. At the general store, Danny asks that he do something for him at Erik's.
Talking to Stella, she may mention a strange plan growing around the clock tower. If Raguna waters it, it will immediately grow into a giant bean stock, allowing Raguna to climb it to Whale Island. The whale greets Raguna and begs him to help restore the runes inside of it so it won't lose its ability to fly, causing the destruction of the town.Talking to Mist, she again mentions the voice calling to her and says that it will talk to Raguna as well. That night, a voice calls begging for help and saying that a power is coming from somewhere.
Trampoli seems like a peaceful town, but it's actually in great danger. Above the town, there is a floating island in the shape of a whale, which his held in the sky by an enormous number of runes. Although it is still aloft at the beginning of the game, the runes on the island are vanishing. If the problem isn't solved, the island will fall and crush Trampoli.
How to Progress The Main Storyline
After you move in talk to Mist and Stella every day. This should trigger some events. First is Stella requesting for you to deliver things to people in town, Eunice first, after you finish all of this you should know a lot more people. Second, it involves both Mist and Stella. Mist will comment on having a dream where she climbs a bean stock to Whale Island. After this, if you talk to Stella, she will comment on a strange plant that started to grow by the Clock Tower and will say that you should water it. If you water the plant, then it should instantly grow to a giant bean stock that you can grow to Whale island.
Another is when you unlock the Green Ruins. Mist will request that you cut down the grass in the yard with a sickle. If you do, you should find stairs leading to the Green Mines. There should also be one from Mist where Raguna asks Mist why she came here and she will tell him that she heard someone in calling her in her dreams who was in pain, so she came here to look for him, and tells Raguna that the next time she hears him she'll tell him to come to Raguna in his sleep. The next time Raguna goes to sleep, there should be a scele-like event where someone asks Raguna for help.
Once you beat the Green Ruins Boss, a giant Clucky, you will get a rune-stone-ish looking thing that you will insert into the tree on the Mountain Road to unlock the Lava Ruins.