|Spoiler Warning: The following may contain important spoilers about characters or parts in the story.|
The game begins with the protagonist on a flying ship heading to Selphia to deliver something important to Ventuswill. Soon afterwards, however, two men dress as soldiers emerge from barrels, aiming to steal what the protagonist was keeping safe to deliver. A battle begins, and after winning one of the soldiers threatens the protagonist, only to hit them on the back of the head, giving them amnesia. Thinking that the protagonist was only pretending, the soldiers threaten to toss them off the airship, only to accidentally knock them off for real. They fall a great distance, onto a large dragon's head. After confirming that the protagonist had amnesia, and putting them in place of the arriving Prince/Princess, they are arranged to live at the castle.
The next morning, one of the castle's butlers Clorica(for Lest) or Vishnal(for Frey) wakes up the protagonist and tells them that even though they are of royalty, those who do not do work don't get to eat or stay in the village. This gives a short tutorial of how to farm.
After that, the protagonist goes back to report to Ventuswill, only to find that the real prince of Selphia, Arthur, has just arrived. Ventuswill will then freak out about her mistake and tries to put the blame on the protagonist, but after some explanations are made, Arthur tells them that he wouldn't mind them helping him out with managing the town, even if it's against his father's wishes, since he's against leaving you out on the streets with identity problems. This goes into another tutorial about Prince/Princess Points and how to use the Order Symbol.
In a forest to the east of Selphia is Yokmir Forest, and upon entering for the first time, the protagonist comments on a swarm of butterflies that seem to be leading them deeper into the forest. Following the butterflies, they come to the back of the forest, where a large, butterfly-like monster named Ambrosia is waiting. Upon defeating the boss, a little girl will take her place. Shocked, the protagonist takes the girl to Jones, who looks over her in the clinic. Within a few days, she wakes up and introduces herself as Amber. She lives with Illuminata and helps with the flower shop after she has woken up. Talking to Ventuswill about her hints that she knows something about the girl, but doesn't say anything.
Several days after Amber has woken up, the villagers will begin to talk about a screaming that could be heard. Because of the help the protagonist had been before, Ventuswill asks them as a favor to personally see what's going on. Just to the south of Yokmir Forest is the Water Ruins. When the protagonist is about to enter, Doug comes up from behind them, telling them not to trust "that fool." At the heart of the ruins is a black, war horse like creature by Thunderbolt, and like before, after defeating the boss, a person appears in its place. The man, Dylas, goes to live and work with Porcoline upon waking up, despite his protests.
As days go by, once again a rumor will be spread around about the appearance of ghosts near Selphia, and a girl who appears in the houses and streets of Selphia seek out the protagonist for help to save "Dolly". This takes the protagonist to the Obsidian Mansion, where moving through the mansion ends in a theatre of sorts. Here, a boss named Marionetta resides, and once again upon being defeated, a girl takes their place. Once waking up, the girl, Dolce, who is always accompanied by a ghost girl named Pico, moves in with Jones and Nancy and helps them run the clinic.
During these events and the three moving into Selphia, Ventuswill has been acting strangely, along with strong hints that she knows more than she lets on. After being pressured, she collapses, stating she is sick, which greatly shocks the protagonist. She tells them a good portion of the story, about Amber, Dylas and Dolce, and about how the Runes were depleting. Now that the Guardians were no longer maining the runes, they were quickly running out and Ventuswill was slowly dying. This leads to a conversation about Rune Spheres, and how they might possibly be the things to save her.
Doug, however, is against Ventuswill due to him believing that she slaughtered his village, and vows to get all the Rune Spheres before the protagonist does. A rune sphere placed at where the Guardians once stood greatly improved the rune population. However, one day back in the village, Doug threatens to kill Ventuswill on behalf of his village. After hearing her story and how she couldn't have done it, and when asked if he still wished to kill her, she stops to think about his answer. Eventually, Doug gives the protagonist the final Rune Sphere, saying it was in their hands whethere she was saved or not.
Soon after, though the runes are coming back, Ventuswill still asks the protagonist to bring back the final Guardian, Leon who resides at Leon Karnak. However, it is found out that the Leon Karnak has been infused with the Forest of Beginnings, and that there was little chance of getting there, and even less getting out. This, and Ventuswill's weakness, motivates the entire town of Selphia to try and find a way to get the protagonist to the Forest of Beginnings and back again. After several days of everyone researching, Arthur says that he knows of someone who once went to the Forest of Beginnings, and was trying to get in contact with them. This person turns out to be Barrett, and he gives the protagonists a spell that would be able to allow them to return. However, it only worked once, and if messed up they would be stuck forever.
When traveling to Leon Karnek, the path is blocked by a large Monster Gate, similar to the smaller ones found in dungeons and fields. Once the large gate has broken, the protagonist jumps through just as it's disappearing, getting transported into the Forest of Beginnings.
Going through the path, the protagonist hears flashbacks of each of Guardians--Amber, Dylas and Dolce--just as they are giving up their lives to become Guardians to save Ventuswill. At the end of the path is Leon Karnak proper, where two large fox statues are blocking the entrance to the boss chamber. Upon defeating them and proving worthy, the protagonist is able to continue, where a large sarcophagus is. Upon defeating, Leon the last Guardian is revealed. However, there is an invisible wall separating the protagonist and Leon, and in a last attempt to save him, throws the charm that the return spell must be used with near Leon, and sacrifices their safe return for his. Just as the protagonist thinks they are stuck in the Forest of Beginnings, Ventuswill swoops in and scolds them for being so reckless and takes them back to Selphia on her back.
Once back in Selphia, she returns the memories to the Guardians, who apologize for what they did to upset her so, and continue living in Selphia along side her.
About a week after the events of the Guardians, when entering Selphia Plains the protagonist will hear a scream coming from Selphia Square. A man who appears to be from the Sech Empire is threatening Forte all while outing Doug who had been the spy for their kingdom, as well as revealing it was really the Sechs who had killed his village. He uses the power of the rune sphere to transform into a dragon, which the protagonist and Forte defeat in battle. Once doing so, they retreat, and Doug confesses everything. He reveals that he knows that they have a hideout in Idra Cave, though he isn't exactly sure where.
Finding their hideout, the protagonist comes face to face with Ethelberd, who reveals that he has stolen the Rune Spheres that were placed and were using their power to recreate the Native Dragons. He summons one as a test for the protagonist, and states that even if they do not go after him, he will surely go after them. Arthur tells the protagonist to go to Maya road, where the border of Norad touches Sech. However, the bridge has been burned down by a Sech soldier. After being repaired, the protagonist follows the Sech soldiers into their territory, where they lead them to Ethelberd, who summons another Native Dragon for the protagonist. Once defeating the cloned dragon, the Sechs are seen escaping to a floating empire.
Giving chase, Arthur steers an airship, however it is quickly overrun by Sech enemies, and stalls them long enough to find a clear spot on the fortress where there are no Sech soldiers, and the protagonist jumps down into the area. The place where Ethelberd escaped to is blocked off, and the protagonist defeats three bosses who break off a piece of the obstruction once defeated, which then gives the protagonist access to where Ethelberd was waiting for them.
He uses the power of the Rune Spheres to fight against the protagonist, saying that his power was that of an Earthmate, or a God itself. Arthur and Doug come in on an airship in an attempt to aid the protagonist, however they are quickly shot at and have to try and land safely. It is then that Ventuswill comes to the protagonist's side. This appears to have been Ethelberd's plan the entire time, as he fuses himself to Ventuswill with the help of the rune spheres and becomes even more powerful than before--even for the protagonist.
It is then at they feel Venti's Charm close to their heart, and the Guardians and people of Selphia are calling out to the protagonist, giving them their wishes, cares and power, which is just what the protagonist needed to defeat Ethelberd.
After coming home safely, along with Doug and Arthur who managed to safely land the airship, the town of Selphia throws a party for the safe return of the protagonist and the well-being of Ventuswill.
Later that night, the protagonist talks to Ventuswill, who reveals that even though she was there, her body was already in the Forest of Beginnings, and that she only wanted to talk to the protagonist one last time before the had to leave. She wished to be sent off with a smile, and that she was grateful for all that the protagonist had done for her and for the town. The arc ends with Ventuswill's body slowly disappearing as it returns to the Forest of Beginnings.
- Note: The third Arc cannot be played until after seeing the event Memories.