The game begins with the protagonist riding a flying ship heading to Selphia to deliver a blue orb, which seems to be an important item, to the Native Dragon, Ventuswill. Soon afterwards, however, two men dressed as soldiers emerge from barrels from onboard the airship aiming to steal what the protagonist is keeping safe for delivery. A battle begins, and after the protagonist thinks they have won, one of the soldiers surprises the protagonist from behind and ends up hitting him/her on the back of the head, causing amnesia. Thinking that the protagonist was only pretending, the arrogant soldier threaten to toss him/her off the airship, and the oblivious, dumb soldier accidentally knocks him/her off for real. The protagonist falls a great distance, onto a large dragon's head. After the Native Dragon, Ventuswill, and her loyal butler Volkanon confirm that he/she had amnesia, the protagonist is mistaken for a member of the royal family that is beingy sent to rule Selphia, and is given a room in the castle to sleep in.
The next morning, one of the castle's butlers, Clorica wakes up the protagonist and tells them that even though they are (Supposedly) of royalty, those who do not do work do not eat. She then feeds you apple pie, and sends you into the farm to meet another of the castle's butlers, Vishnal. He gives a short tutorial on 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, he's against leaving you out on the streets with identity problems. This leads 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, he/she arrives at the back of the forest, where a large, butterfly-like monster named Ambrosia is waiting. Upon defeating the boss, a little girl will appear. 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 wakes up. Talking to Ventuswill about her hints that she knows something about the girl, but she doesn't say anything and is hiding something.
Several days after Amber wakes up, the villagers will begin to talk about screams that can be heard throughout the village. Because of the help the protagonist contributed 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.", referring to Venti. (This will be important in later stages of the plot). At the heart of the ruins is a black, horse-like creature named Thunderbolt, and like before, after defeating the boss, a person appears in its place. The man, Dylas, is forced to live and work at the restaurant by Porcoline after 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 seeks out the protagonist for help to save "Dolly". This takes the protagonist to the Obsidian Mansion. Navigating to the end of the mansion will leave the protagonist in a theater of sorts. Here, a boss named Marionetta resides, and once again upon being defeated, a girl takes their place. Once she wakes up, the girl, Dolce, who is always accompanied by a ghost girl named Pico, moves in with Jones and Nancy to help them run the clinic.
Throughout these events, and with the three humans born from monsters moving into Selphia, Ventuswill acts strangely, and it is strongly hinted 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, mainly about their role as guardians while also explaining the depletion of the runes. Now that the Guardians were no longer creating runes, the runes 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 that could save Ventuswill.
Doug, however, is against Ventuswill due to him believing that she slaughtered everyone at his village, (Sechs propaganda), 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, Doug will stop to think about his answer. Eventually, he gives the protagonist the final Rune Sphere, saying it was the protagonists decision whether Ventuswill would be 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 Leon Karnak has been infused with the Forest of Beginnings, and that there is a small chance of getting there safely, and even smaller chance of getting out. This, and Ventuswill's illness, 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 protagonist a homing ring, and a few words that will trigger the ring to allow them to return. However, it only works once, and if messed up, the protagonist would be stuck in the Forest of Beginnings forever.
At the entrance to Leon Karnak, stands a large Monster Gate, similar to the smaller ones found in dungeons and fields. Once the large gate is destroyed, 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 the first three Guardians--Amber, Dylas and Dolce--just as they are giving up their lives to become Guardians to save Ventuswill. At the end of the Forest of Beginnings is the top of Leon Karnak, (You will get to explore the actual Leon Karnak later in the story) where two large fox statues, Sano and Uno are blocking the entrance to the boss chamber. Upon defeating them and proving him/herself worthy, the protagonist is able to continue to the final chamber, where a large sarcophagus resides. Upon its defeat, Leon the last Guardian is revealed; However, Leon becomes airborne and floats in a meditation position, separating him from the protagonist. In a last attempt to save him, the protagonist throws the ring to Leon and says the incantation which sends him back, sacrificing their own safe return for his. Just as the protagonist thinks they are stuck in the Forest of Beginnings, Ventuswill swoops in and scolds the protagonist for being so reckless, then takes him/her back to Selphia with a ride on the dragon's back.
Once back in Selphia, she restores the Guardian's memories, who apologize for what they did to upset her. Life quickly returns to normal and all four live as residents in Selphia along side Ventuswill.
About a week after the events of the first arc, the protagonist will be about to return to the village when he/she hears a scream coming from the village square. A man who appears to be from the Sechs Empire is threatening Forte all while telling Doug to help him, because he had been the spy for their kingdom. As the vulgar man does this, he accidentally reveals that it was really the Sechs army who had destroyed 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 the Sechs have a hideout in Idra Cave, though he isn't exactly sure where.
After finding and infiltrating their hideout, the protagonist comes face to face with Ethelberd, Lord of the Sechs Empire, 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 he/she do not go after him, he will surely go after him/her alongside all the villagers. Arthur tells the protagonist to go to Maya road, where the border of Norad touches Sechs Territory. However, the bridge was burned down by a Sechs soldier in their attempt of escape. After obtaining an airship liscense to cross the gap in the bridge, the protagonist follows the Sechs soldiers into their own territory. They unwillingly lead him to Ethelberd, who summons another Native Dragon for the protagonist. Once defeating the cloned dragon, Terrable, the Sechs are seen escaping to a floating empire.
Giving chase, Arthur steers an airship, however it is quickly overrun by Sechs creations, but the main protagonist stalls them long enough to find a clear spot on the fortress where there are few Sechs 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 each remove a piece of the obstruction once defeated, which then gives the protagonist access to where Ethelberd is 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 even a God itself. When defeating him, he goes into a rage and becomes nearly invincible. It is then that Ventuswill comes to the protagonist's aid. This appears to have been Ethelberd's plan the entire time, as when he is defeated, he fuses himself to Ventuswill with the help of the rune spheres and becomes even more powerful than before. Doug and Arthur attempt to help the protagonist, but are hit by Ethel(will)bert's demonstration of his newfound power, a raging tornado.
It is then when the protagonist feels Venti's Charm close to their heart, and the Guardians along with the people of Selphia are calling out to the protagonist, giving them their wishes, power, and desires. The protagonist then receives an immeasurable amount of strength and defeats Ethelberd who goes psychotic and is then slowly pulled into the Forest of Beginnings.
After coming home safely along with Doug and Arthur, who also 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 tells them that even though her body is in the castle, her spirit is already in the Forest of Beginnings. She also says she wanted to talk to the protagonist one last time before embarking. Venti wished to be sent off with a smile, while saying 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. One easy way to trigger them is to bring both Dylas and Amber into your party, then sleep. If they both leave in the morning, then the memories event will follow shortly. The event starts with Amber and Dylas in the middle castle room pondering ways to bring back Venti, while the protagonist eavesdrops.
The following day, Dolce converses with Raven in the Bell Hotel. Raven refers to her as "A Regular" and Dolce asks Raven if she knows about anything useful that could help bring Venti back. She then tells Dolce that she does not know of anything that could help, then Dolce leaves, but sees you on the way out.
The day after that, Leon will talk with Barrett in the Bell Hotel, and Barret will explain that when he first made the homing ring, it was by luck and he didn't even know how he made it.
Once again, another day passes and then Amber, Dylas, Dolce, and Leon stand in the middle of the castle when the protagonist (Finally) consults them. They describe the situation to the protagonist, and then wonder what they can do at this point. The protagonist will eventually be forced to choose the option where you suggest using "Omni Gate". The 4 of them express worry, as before when you tried, you nearly incinerated yourself in an ensuing explosion. After arguing with the protagonist, they agree to let the him/her use Omni Gate, but they settle on one term - they have to supervise you.
They give the protagonist time to prepare, and when he/she's ready, you talk to Leon to begin. And, of course, another explosion occurs knocking protag-kun unconscious causing him/her to be carried to the clinic. Then the idea of going back to Leon Karnak is roused and they send protag-kun up to Leon Karnak. He/she proceeds up the tower fighting many a foe, plus a Grimoire, until finally you reach the top. Sano and Uno ask what has brought him/her to ascend to the top of the tower. Protag-kun will then say they came to test their mettle. He/she beats them and proceeds down a set of stairs to fight a sarcophagus. Upon defeat, the protagonist hears a noise, which enables them to enter the Rune Prana through the center gate of Leon Karnak.
The Rune Prana (Hell) consists of 7 sections with many powerful foes and traps to send you back to Jones. Have fun splurging your life savings. In the first area, a Bane Dragon will have to be defeated, in the second, an Octopirate, in the third, a Crystal mammoth, in the fourth, the mythological beasts Hinoe and Kinoto, in the fifth, the bewitching Siren, in the sixth, the return of Death Wall, and then finally, after having your ass brutally smacked around, you reach the last room where you meet Ragnarok.
After defeating a boss, a short room after every area gives Lest fragments of his Memories back, but upon Ragnarok's defeat, you enter a small segment where you call for Venti and she responds. The protagonist then tells Venti about using himself as a Vessel, but when the protagonist shouts, "ETHERLINK!", Venti disappears and you're left with a dimly-lit rune sphere.
Afterwards, one must use escape to return to their room. Then, one can go to the center of the castle to pay tribute to Venti, who has returned. After thanking you (and scolding you for the harm you put yourself in), you are free to do as you wish - be it complete quests, get married if you haven't already done so, ship everything, etc.
- Note: 90% of Rune Prana has no dialogue.