- In Chapter 3 (The Sage who Became a Star), things get very sad after Lin wakes up. In this chapter, you must, at first, find a way to wake the apprentice of a famous Sage called Crest, who died some months prior to Max's and Monica's arrival while trying to protect a great magic crystal from Gaspard. The flashbacks of Lin and Crest are absolutely beautiful, but what really did it was his death. And even more, Lin talking to his corpse that he was the only sage for her.
- Despite being a Foregone Conclusion, the end of Chapter 4 can still be quite sad, when Shingala must leave Pau to be with her own kind. Granted, this scene may also be sad just at how you remember seeing these scenes play out.
- Dr. Jaming could be quite sad - given how he zonked all the sea creatures to attack you, and their first response after the mind-control helmets are removed? They lick him.
- Gaspard's final battle and death. After Max defeats him, he shares his backstory with the heroes in a deliberate Not So Different moment, pulls a partial HeelFace Turn (he basically decides to become neutral) and wishes them well on their quest, and prepares to leave the conflict. Then Emperor Griffon pulls a Villain Override on Gaspard and forces him to attack Max and Monica. After that battle, as Gaspard lies dying, he ruefully says he won't be able to see the end of their journey, and Monica, who had until then hated him for killing her father, grieves for him and curses Griffon.
- As you run through Chapter 7, you get flashbacks that define Griffon's backstory: He came to the Moon Flower Palace with no memory of his past, attempting to look at the flowers. He almost gets reprimanded, but the Palace leader, Alexandra, takes him in and has him watch over the flowers, because of how much he likes them. They develop a great bond for each other, but a great war ravages the area soon after, including the palace in its destructive wake. This war takes Alexandra's life, and all the plant life in the Garden dies soon after. Griffon, in his anger and pain, vows to destroy humans, so that something like this could never happen again. And finally, FINALLY, when you have to fight him, you are wondering how to save him. And then, right when you think you saved him, the apocalyptic scenario predicted by Griffon and the Ancients activates, and the moon comes crashing down. Griffon (whose true name is Sirus) is the key to stopping this, but he has to give up his life... This game really, REALLY loves that trick. It loves to actually make you sympathize with the characters, and then kills them off as soon as you save them. It really hurts, Level 5 really wants to pull on your heartstrings.
- Part of the ending. Max is reunited with his long-lost mother...but she can't stay with him in Max's time period and must return to her own time.
Tear Jerker / Dark Chronicle