Given how this game revolves around trying to Set Right What Once Went Wrong through Time Travel, only to learn that not everything can be repaired so easily, it's hardly surprising that it can prove tear-jerking at times.
- Rexwood was named for its hero, as its residents are quick to brag. What they're not so eager to share is why he became a hero: he went to fight the monsters and expected the other residents to follow and back him up. Everyone chickened out, leaving him to battle on alone, waiting for reinforcements that never came. And he won, only to die from his wounds because nobody was there to help him. No wonder Matilda holds a grudge.
- Then after you kill the Boss, you have to kill Matilda because she followed her brother and saw his victory and death. Monsters then took her sorrow and changed her into the Real Big Boss of the area and you cannot reverse the Island's curse while she lives.
- Dialac is incredibly depressing. Its tale is told almost entirely by visions your hero receives after touching the bodies of its residents, who were all turned to stone by the Gray Rain.
- Clayman, the strongman of the village, travels away to get water for the desert village while they pray for rain. The cursed rain turns them all to stone and he mourns not being petrified too so he stays around the village alone with the statues of his friends for 50 years.
- Even worse is the fact that the main character is awoken by the Soul Moans of the petrified villagers and has to see their most treasured thoughts from the day they were petrified. Made even worse than that when one of the statues disintegrates by you doing that.
- In the 3DS version, only a handful of statues glow at night: the ones who have information relevant to your quest. Compared to the original, where everyone glows/gives you a chance to see their last moments alive, it adds to the sense that the residents of Regenstein are so far gone that they can't even pass on their stories anymore.
- Furthermore, Clayman got the cure from a traveler. He never used it because the statues had eroded from long exposure to the elements. Use the cure anyway and a little boy is rescued. Narration on a black screen covers the boy having everything explained to him; before you leave, you can find him standing in front of the petrified remains of his best friend, still trying to wrap his mind around the fact that that's her...
- Eri. A malfunctioning Mechsoldier who gets adopted and re-purposed by Zebbot into a Robot Maid and a weapon against her own kind. Despite being key to saving the kingdom of Falrod, the villagers respond by blaming her for everything, even beating her when she doesn't fight back. On top of that, it's made clear that Zebbot mainly sees her as a tool, a Replacement Goldfish for his late fiancée, Eri. To top it all off, when you return to Falrosh in the present, you find she's spent all her life in his isolated shack, caring for Zebbot... or, rather, Zebbot's skeletal corpse, as she can't tell that he's passed away ages ago. Then the current ruler finds her, and has his court researchers take her apart piece by piece to see how she works. When Trad's descendant tries to help you free her, she mistakes him for Zebbot and tries to take him back home, leading the king to label her unstable and return her to Zebbot's cabin. She thanks you for this, and finally winds down shortly thereafter.
- Verdham has its Love Dodecahedron, best described as a comedy of errors: Linda, the center of this whole mess, has to shoulder her parents' debt to the richest man in town after they pass away. Borlock learns that his son Iwan has fallen for her, and so offers a compromise: he'll forgive their debt if Linda marries Iwan, However, Linda actually loves Pepe, who works for Borlock and Iwan as a gardener along with the rest of his family. Linda and Iwan's maid Kaya pressure Pepe to fight for her, or elope — but even though he loves Linda more than his own life, he can't bring himself to abandon his family to whatever vengeance Borlock might visit upon them if their son steals away his son's fiance. Eventually, he chooses to leave Verdham for good rather than choose between his lover and his family, leaving behind everything he cares about in a last-ditch attempt to please everyone. ...It doesn't help much.
- Kiefer attempts to help by pointing out how he could talk to Borlock and find some other way to settle the debt. Pepe acknowledges this, but sadly adds that it's too late, and that he's too cowardly anyway... echoing what Linda said to him when trying to provoke him into acting.
- Later, you get to revisit Verdham several years down the line, and learn how everything turned out. Linda married Iwan, but never stopped pining for Pepe, and eventually abandoned her family to go search for him. Her son, Eppe, learned about this beforehand and begged for her to take him along, but she refused, leaving him to look after Iwan despite him already despising his layabout father. Iwan squandered Borlock's riches, and wound up indebted to the new richest man in town, still retaining his lazy nature and leaving Eppe to shoulder the brunt of the work. Meanwhile, Kaya married the new rich guy, playing the doting wife while plotting to slowly poison him, letting him think he was dying from some mysterious disease and thinking the poison she mixed into his food was actually medicine.
- To top it all off, Linda finds Pepe... but is so ashamed of abandoning her family to find him that she never even talks to him, instead joining a convent and watching over him from afar. Pepe only learns about this after her death, and breaks down upon seeing her grave and reading her epitaph.
- The Nintendo 3DS version handles this a bit differently as in Lavander/Linda and Carraway/Pepe are both dead and buried side-by-side at the church, giving their story a somewhat Bittersweet Ending as they are now Together in Death.
- In fact, one of the biggest surprises you have is when you go to the town in the present, you find that it's no longer there, and the other town is around. Once you have gone there in the middle, the name of the new community hits you: Wilted Heart.
- Layla and Jann's story. Yeah, Jann's a Green-Eyed Monster who doesn't care for Kiefer getting closer to her, but then you help the Deja Tribe hold their ceremony... and it doesn't work. Then you find out why Jann's been so dead-set on pushing forward: at some point, a divine birthmark like Layla's appeared on his body. According to their tribe's customs, that means that he and Layla can never be together... unless they'd completed their duties. He'd hung all his hopes on this, and it was All for Nothing.
- All Zaji wants to do is protect his ill sister Neris... and all Neris wants is to not be a burden to others. The fact that they got trapped in a penal colony where the only way out seems to be making a Deal with the Devil doesn't help. It gets worse when Zaji takes a blade in the back for her. And the Trauma Conga Line doesn't stop there for either of them.
- The kicker has to be when Neris gets her soul sucked out and is forced to fight in the monsters' arena for their amusement, wielding the very blade holding her soul. Zaji knows how to fix this, having gone through the same thing himself — the trick is running the victim through with the SoulSword housing their spirit. Which he does. Before the monsters drag him away without giving him a chance to see if it worked or not.
- And how does it all turn out, once the temple is liberated? Zaji takes up the warrior class, only for Neris to snap and cry that she doesn't want anyone else to suffer for her sake. Zaji responds to this by deciding to leave, giving Kasim permission to look after her in his place. It's also heavily implied that the whole ordeal put too much strain on Neris' body, shortening her lifespan even further...
- Then there's Dune/Al-Balad, where most of its strongest citizens have been enslaved to build The Sphinx/Likeness — which was meant to ward off evil rather than strengthen it, as its purpose has been twisted by Lord Seto/Setesh, who turned it into a statue of Orgodemir. When you first arrive at the refugee camp, you see a nameless villager strike out into the desert, choosing likely death there than living in complete misery. Things go downhill from there.
- Perhaps the darkest moment is when you're sent to find some sign that the legendary Tyrannos/Great Serpent of the Nihil still exists and can help carry you to the Sphinx... and return with a fossilized skull. Zarathustra/Khalid takes this as proof that there is no hope, and falls into Death by Despair.
- Then there's Queen Fedel/Fertiti's reaction when you finally meet, and she learns what has become of her people... She nearly crosses the Despair Event Horizon herself, realizing her surrender and cooperation with Setesh was a Senseless Sacrifice, as she believed it would protect everyone and He Lied.
- Sieble/Buddy of Loomin/Nottagen. For starters, the town he lives in is a Doom Magnet. First time the heroes go into the village, he has been kicked out of his house and lives on the streets. Poor guy just wants to be left alone with his exotic pets, but they both sacrifice themselves to save him. Though the latter case only occurs if you don't kill Chibi yourself.
- And if you did kill Chibi, he ends up the Sole Survivor of the Hellworm raid aside from your party, as the lot of you huddle in a well until the sounds of slaughter overhead fade away...
- Even the 3DS version makes this sad if you save Chibi, because Buddy has to follow you and abandon Chibi, who even walks after you confused. Then, out of nowhere, Chibi returns and fights off the hellworms.
- Gorges has Firia, resident poster child for All of the Other Reindeer. Gorges is populated almost exclusively by the Winged Humanoid Lefans; little Firia is the only exception, an orphan adopted by their current leader, Pendragon. The adults all regard her with pity, while the kids bully and belittle her — particularly her younger sister, who treats her like a servant. Only her grandmother treats her as something other than an object of pity and derision; her father does absolutely nothing to protect her, and won't even scold his daughter for treating Firia so poorly. The bullies eventually strand her on a narrow ledge, and she almost falls to her death, only surviving because her grandmother gave her the BlissRock. After this, Grandmother Pendragon calls out Firia's father, and reveals Firia isn't an orphan, but Pendragon's daughter by blood. She just happened to be born without wings, and her cowardly father was afraid he'd lose his position if people knew he'd fathered a wingless child, so he pretended he'd just adopted her and turned a blind eye to her suffering.
- Everything about Labres. You've got Lucas, who was just orphaned when his parents tried to help the priest deal with the monsters casting a fog over the town. Then there's the fate of the priest himself: he made a Deal with the Devil to be transformed into a hideous monster; in trade, the real monsters would leave Labres alone for as long as the polymorphed priest lived. However, the paranoid villagers only see a hideous beast mocking the church by moving in, and decide to lynch him. Oh, and it turns out you met this particular priest before — in Probina, where he makes a Heroic Sacrifice to save your party. Thank you, Timey-Wimey Ball.
- And in the present day Labres, they've chosen to whitewash the truth about what happened, replacing the Monolith telling their tragic tale with one painting the townsfolk as the 'heroes' of the whole mess. It's incredibly depressing to see Lucas' descendant getting the All of the Other Reindeer treatment from the other kids just for telling the truth... Or hearing the kids talk about how their parents are punishing them for telling the truth after they read the original Monolith. On the bright side, this does lead them to befriend Leif and continue to tell the truth about the town's history no matter what their parents say.
- Coastal's even worse than Labres, given how it was punished for helping the heroic Sharkeye try and fight back against the Demon Lord... Every time the moon is full, any newly-born children transform into monsters and run away, visiting their helpless parents a few more times before leaving for parts unknown. When you arrive, you get to witness this firsthand, with the victimized parents completely breaking down...
