The aftermath of the Alien Abduction. You hurry back to Panselo Village, and find that everyone is gone, even the animals. The children are all rightfully scared, and those that didn't see the ship appear all freak out upon being told that they were all taken by aliens.
After everyone's settled down, some of the children wonder if they were really lucky to be left behind or not since there's no adults to look after them, and those who weren't part of the orphanage will spend the night there so they're not alone.
The following day, everyone tries to carry out the tasks that the adults would usually do because someone still has to keep everything going, but some of them admit that they're using it to distract them from the sad situation.
If that wasn't bad enough, a Dark Reprise of the village's usual theme plays on the first day after the abduction. It really gets across the fact that the village is almost empty, and how uncertain things are.
Lisa tries to claim that she's fine with being stuck working with Pooki in order to pay off a debt she somehow acquired, but it's clear that she isn't. No wonder Gail wants to help her so badly.
There's a sidequest later on that involves figuring out how to open the safe in his parent's room. Inside you'll find some letters written by his parents, each intended to be opened on his birthday for the next fifty years. It's implied that they knew they would die because their decision to leave Rhodus and join Castella would be unpopular, but still wanted their son to know he was loved.
After freeing Lisa, Gail tells her about what happened on the way back to their village. Lisa admits that now she doesn't feel so happy about returning. She also tries her best to look after the children there, saying she'll give them emotional support if they need it, and later lets them do whatever they like in case they don't survive the invasion.
One of the first things you see when you enter the main upstairs area of Thomas' lab is several pictures of him and Rutea, showing how close they once were. Additionally, one of his logs mentions that he feels like they're growing apart. And then Gail has to tell him she's been abducted.
If you talk to Rutea at the beginning of the game, she'll mention that Thomas was asking if she wanted to come and work with him in Daea, and wasn't sure if she should do that or stay in Panselo which she's more used to. You can tell her that she should go, which she'll agree with... only to never get that chance due to the abduction happening.
Despite learning about what happened to his sister, Thomas manages to stay level-headed about it and focus on warning the King after Bart says the world is in danger. When returning to Panselo after you rescue Prince Leo, he immediately goes to Rutea's lab, where he admits that it's only just starting to sink in that she's really gone.
When you visit the lab the following day, you'll find that he's moved Rutea's picture of the two of them (which he has a copy of in his own lab) to the basement where he's set up a bedroom for himself. It's also implied that he read through the book that she wrote poems in, the first of which is about how much she looks up to him.
The reveal that Earth is going to be invaded and destroyed. What makes it worse is the fact that neither the Astral Empire nor the Galactic Federation seem to acknolwedge that the planet has improved after the Great War, and that it being destroyed would make humanity's efforts to restore the world all for nothing.
Bart also says that even though the villagers were taken by space pirates who want to sell them since their species will be considered rare if their world is destroyed, they are actually safer than everyone who was left behind. As much as everyone wants to save their loved ones, they have to put it on hold to save themselves first.
Not much detail is gone into, but it's implied that Leo's parents were killed when the Kobolds took over the castle. Despite this, he manages to avoid breaking down over it and helps however much he can.
Cosette is said to have once been more populated, until a plague broke out and caused a famine that drove many people away. The music that plays on the overworld is slower and sounds more bittersweet.
Gail's rival and Ernest's older sister, Aella, is found in Cosette Village with amnesia. The quest to help her remember who she is culminates in you learning the Prelude of Panselo, a song that is said to be known by most villagers, and that Ernest says she used to sing to him. After regaining her memory, she decides to wait until she returns, and it's implied that Gail hasn't told her about the abduction likely so she won't worry too much.
The journey beyond the First Wall. The music that plays both in the overworld and at the Last Wall is probably one of the most somber on the soundtrack, and heavily contrasts to the lively music that plays at the First Wall.
At the Last Wall, you meet an NPC called Hilde who asks you to bring back the dog tags from the fallen soldiers in the Scorched Lands, a place that many guards are said to not return from, so that their friends and family members can have closure on what happened to them. One of them will turn out to be from her lost lover, Alba. She also admits that returning the tags to their families will be painful for them, but feels like it should be done.
There's another sidequest where Sir Wallace mentions that one recruit got past the wall, and is worried about his safety since he's unsure if he's suited for serving at the Last Wall or not. You find him near a holographic advert that you have to turn off to get him to leave. After bringing him back, Wallace decides that he can serve at the wall after all, but the guard himself isn't too happy about it, saying he preferred the fantasy of the advert.
The Scorched Lands. There are remains of more modern buildings seen everywhere, showing what the world was once like, and you also see many dead bodies of guards who were killed by all the dangerous machines.
If you backtrack to the Anuri Temple after getting more items you can unlock some additional areas, one of which is more dimly lit and has sad music playing. There are even more skeletons of the Anuri than the other parts of the Temple, and the song that plays here is called "Song for the Dead".
You learn from submitting the Lunar Vase to the antique collector that the Anuri were a race originally created to fight in the Great War, but continued to live afterwards, until they went extinct for an unknown reason. You also learn from submitting the Lunar Frog that they lived similarly to humans and even had their own toys, which said artifact is.
In the Subeterra area you can find an Anuri, who the Oracle says is the Last of His Kind, with the same music from the second part of the temple playing. He is very sad until you give him the Strange Urn (obtained from unlocking the back of the temple and fighting the Century Toad), which is then dropped into the water; if you exit and enter the room again, you'll see there are now tadpoles in the water, suggesting that the race isn't completely gone.
One of the messages in the Ancient Vault is from some parents whose child had an illness that couldn't be cured, so she had to stay in there for longer until it could be. It's unclear if that eventually happened or not, but the message tells her not to worry if her parents look older when she wakes up.
If you give Fran the maximum amount of Moonstones you can give her, and also free Floret and Gilroy, there will be a cutscene where the two come to visit Fran and tell her that she can't open the Franway to the public because it would cause problems in the economy, and that they only let her work on it so they could use it for themselves. Fran feels betrayed and runs off crying, which also upsets Gilroy (who is only a kid), and even Floret feels uncomfortable and decides to bend the rules and give Fran some more time.
In E.D.E.N, there are several computers where you can read messages left behind by some people who were given the task to help make the planet habitable for human life again, working under Grasso who, unlike in the Flash game, died before the events of the remake. They are shown to have lived as normally as possible in Pristine City even though most of the population are Golems, and two of them even got married.
Grasso is implied to be a metahuman of some kind, as one of his personal logs states that he outlived the four scientists, whose graves can be seen if you unlock the outdoor area to the right of the city. Even though they lived to old age, he was still upset about it, and is implied to have travelled to Aurantia and eventually died himself while over there.
Speaking of Aurantia, while some of the Trolls and Harpies are welcoming of Gail, others tell her that they don't fully trust humans in case they cause more wars.
An optional flashback scene in the secret room in E.D.E.N shows when Gail and Kitt were first brought to Panselo by a woman named Ava. She was a Peace Minister whose work is implied to have gotten her killed, as she had to quickly leave the village and never returned, with the implication that she knew she would die. After losing all three of her children, Nana felt like she'd failed as a mother, and saw the oppurtunity to raise Gail and Kitt as a second chance, eventually opening an orphanage for other children with no one else to look after them.
Even though she believes that Gail must be killed for disobeying her, it's implied that Mother Computer is just doing what she was programmed to, and sees all the Phoenixes as her children, mentioning that she got upset when Gail and Kitt were stolen.
The ending scene shows that while Gail and Bart managed to stop the invasion with the help of the Phoenixes, the war isn't over, since now the Astral Empire has taken an interest in the Phoenixes and wants to use them for themselves. Additionally, the abducted villagers are still missing, and while Gail now knows she's a Phoenix, it's unknown whether Kitt also found out he was one or not while in space.
After the credits, you're shown some artwork that changes depending on your completion level. A low completion level features only Gail overlooking the village. Even if you get a high enough level to show everyone, Gail still stays where she is rather than join in with the other characters.
