The game starts with 3 characters hunting some Soldier Boars at a local, Geeno, Myura, and the Hero. Some silly banter occurs between them. Myura and Geeno are related, Myura being the oldest of the 3 and often calls Geeno an idiot. After they finish talking they enter the fort to take on the boars, battle introduction starts. After completing that a short cutscene occurs where Myura and the hero talk about the tree being a bit unique in that in the entire time they've seen it, it's never flowered or had fruit. It's rather mysterious to them, perhaps special but they shrug it off and head back to the settlement.
On the way back to the settlement, they encounter the village elder/leader/chief. He's going to a nearby town to discuss some issues with the leader there, specifically in regards to getting ready for the coming of the Centennial Fiend (as I recall anyway, I just got up). They chat for a bit and he asks the 3 of them to guard the village while he's gone and they leave. The three then head into town and explore a bit before heading back to rest at their place.
The following day, they wake up to find out that a small regiment of troops from the Aionian Empire is marching towards the village. They haven't had very good relations with them and they're worried that if they left them into the village while the leader is gone, they could forcefully take over or if they don't, they could have reinforcements come later and take the village after squatting while the leader returns. The trio head off to ask them to leave.
They run off to the Easter highway and encounter the soldiers and their leader, Dukass. Some antagonistic talk starts off the conversation with a bit of bantering mixed in. There's mention of a skirmish a few years ago that claimed the life of Signei, the hero's mother, and is part of the reason why there's some animosity towards the Empire on the part of the trio. After digressing a bit. they return to the main issue at end and the trio asks Dukass to have his soldier's go back because the mayor is gone. The soldiers themselves object but Dukass thems not to worry about it and that trying to fight through a powerful swordsman and magician would be a pain in the ass. So they decide to fall back. After leaving, the trio remark that Dukass was extremely skilled and he was actually bluffing for their sake to his subordinates.
With the soldiers gone, they decide to head back to the settlement when they sense the presence of a monster they've never encountered before. They turn back and see this weird purple thing with 4 legs, a huge mouth and no eyes. They suspect this is the Centennial Fiend that was due back now and they get ready to fight it. Before beginning they tell Geeno to run back to the settlement and warn them. He tells them he'll be back with help and runs off. The monster starts spitting out little butterfly critters and they engage in a fight with them and finish it. However, the monster just spits out more and they try to fight again but can't keep up with all of those critters. So the two of them make a run for the fort. The monster gives chase but stops after they arrive there, clearly showing some kind of reaction to the area itself.
While taking a short breather and discussing how potentially dangerous the situation is, and noting that the monster didn't follow them, they realize that the tree at the fort had flowers on it now for the first time ever. They go to investigate and remark at how strange it is when they meet a dark-skinned, white-haired boy in a white robe. He introduces himself as Zephon and tells them that he has a way of helping them and giving them the strength to defeat the monster. He gives the a gem and tells him to touch a tree. Myura is suspicious of the boy but the hero does it anyway. The tree starts to glow and they're engulfed in a white light.
When the light disappears, they look around and think nothing happened. However, when they turn around, they realize that the fort's walls are all intact and not disrepair like it normally was. Zephon mentions that this is 100 years into the past. Myura dismisses this as an illusion but they go to investigate.
When they go looking, they encounter a young man who calls out to them. He immediately recognizes the hero's style and posturing and says that he's a Blue Flash style (or whatever fancy translation you want) swordsman like himself. He thinks this is strange though as he would know other practitioners. He introduces himself as Towald. The hero and Myura are taken a back as that's the name of the Hero from a century ago that defeated the Centennial Fiend.
Myura thinks that this guy might be in on the scam with Zephon but the Hero notices the short sword that Towald is carrying. It's the very same sword he got from his mother, who said that it was a family heirloom passed down through the family line. Towald mentions that he got it from a master swordsman/smith (don't remember which off the top of my head) and he hadn't heard about another. But when Myura looks at it closely, she realizes the two swords have the exact same remarks while Towald and the Hero confirm it. It's the very same sword. This confirms that they traveled 100 years into the past like Zephon had said.
Realizing the luck they have, they tell him of the situation and ask him to help them defeat the monster. They go to the tree and Zephon says, "Oh, he's going with us? Well, I guess it's all right." and they proceed to touch the tree. When the white light dissipates they don't see Towald and Zephon mentions that the Generation/Epoch Tree doesn't take people forward, only backward. He goes on to explain that nothing comes forward, not even items. Myura complains and says it's hopeless and that they can't defeat the monster. However, the hero has an idea and they decide to go back.
The arrive and apologize to Towald about not being able to take him to the future and blames Zephon for not telling them earlier (Zephon's been playing with them). Towald fully believes their story now. Afterwards, the Hero asks Towald to teach him swordsmanship so he can defeat the monster as no person or item can travel to the present. Towald agrees and and estimates it'll take 2 or 3 days to complete the training. They go to learn the technique in the forest as Towald needs real enemies to do so. At the bridge outside of the fort, Towald mentions the soldier boars were in abundance right now and had to be taken care of. Myura and the Hero comment that they were still a problem in the past and must be the reason why the fort was all busted up. Towald takes notice of that but decides to continue on. They engage the boars and he shows off the technique several times with the Hero imitating him. After only 3 battles though, a light engulfs the hero and he learns the technique for himself. Everyone notices this and mentions at how odd it is. Zephon says that he knew it would happen and Myura gets made at him. Zephon just says that she could learn techniques too as Towald likely had a magician in his group as well. After a bit more bantering they head to the tree and jump 100 years to the future.
When they get back, they realize the fort walls are fixed like in the past. For an instant they think they're still in the past but Zephon says this their time. At that moment, Aunt Lurusa comes looking for them and asks them what they're doing. They're taking aback as she should've been at the village. She just mentions she's in the kitchen at the fort like she always is. They aren't sure what they're talking about but will sort it out later as they need to take care of the beast. Lurusa tells them to get magic stones from Geeno's workshop which surprises both of them but they do and then proceed to go fight the monster.
Using the technique he learned from Towald, the Hero cuts through 3 waves of the monster butterflies and runs to the village with Myura. When they reach the area, they realize that the settlement is in ruins and bodies are strewn all over the place, they were too late. A voice calls out to them and they find Geeno propped up against a wall, bloodied. He comments that they finally got here. They tried what they could to stop them but failed. He makes a few more comments after telling the Hero to take care of his older sister before dying. Myura tries to keep him awake but when she realizes he's died, she cries and screams at the top of her lungs.
After recovering they run out of the village and decide to go find the village leader and inform him of what's going on to prevent more deaths from happening. Zephon shows up and makes an somewhat inconsiderate comment and the two berate him for it. He then tells them that they're forgetting something. They can change the past to prevent this from happening. The tree (the only item that seems to not be affected by the limitations) prevents the monster from entering the fort so why not try that? The realize that this could be possible as the fort walls were fixed and go to take a sapling from the tree to do so.
They rush into the past and see Towald again who wasn't expecting them back so soon. The Hero and Myura say that they'll talk with him later about it and rush off to plant the tree. As they leave the battleground they were fighting in earlier towards the settlement, a white light engulfs them and they're returned to the present near the tree again. They go once more into the past and berate Zephon for not telling them. He says he would if they weren't running off all the time. They get thrown into the present when they wander off too far from the tree as it's the tree's power that keeps them in the past. Unsure of what to do, Towald says he can plant it for them because he isn't restricted. He tells them to hurry up and head back to the present to see the results and wishes them luck.
They head back to the present and rush off back to the settlement. They find the tree is in full bloom and are amazed. Then a voice calls out to them and it's Geeno. He complains that they're late but Myura just rushes him and gives him a huge hug. He protests but she calls him an idiot. The Hero just says to let her do what she wants. After wards, the villagers come out and talk to the pair. They can't believe they chased the monster away. After some talk everyone leaves and then Lurusa runs up talking about the seeing the town destroyed and then it being back again. They tell her she's tired and to go rest, worried that she saw what happened there like they had.
The two look at the tree and the hero voices a few reservations about what he's done. He's not really sure what but he feels something. Zephon shows up and tells them that they don't have to be guilty of anything. He mentions the concept of the Million Worlds. It's not really a million but a concept to explain the infinite number of worlds out there and that theirs is just one of those. What happens is that when you go into the past and change an event, the present that you changed doesn't get erased. It continues on but the present you experience branches off. It's similar to how a tree has branches that split off after being broken or changed. Rather than not existing anymore, a new branch comes out. He then goes on to explain that normally time-travelling would cause a paradox would occur where they end up erasing the reason why they needed to go into the past and it couldn't be resolved without the use of the Million Worlds cnocept. He tells them they don't have to feel guilty about anything and just keep on.
The two don't really understand what Zephon is saying but he just says to not worry about it too much and do what they need to. Zephon sets off to do some other business leaving the two to do their thing. He tells them to take a sapling from this tree just in case they need to use it in the future because it'd be a pain in the ass to come back and get it when they need it before he sets off.
Myura and the hero talk a bit more and decide to go find the leader and tell him what's going on when he comes back with his group. They describe the situation and he mentions that he didn't expect for it to happen while he was away. he then asks the kids to go to the village he was just at and discuss getting their security precautions sped up in case the monster should attack the neighboring village like it did with theirs. He says to take Iria with them to get the talking down faster. Myura mentions that Iria is that village leader's daughter though Iria says that she's not related by blood. Iria joins the party and they set off with Geeno heading back to his workshop to make more magic stones.
