- The story of Pedro and Gonzales. They were lucky enough to find Daccat's map and planned on finding his treasure, only to get attacked by Black Pirates. Gonzales got stranded on a tiny island where he finally died of unknown causes. Pedro ended up in Nasrad where he waited on his friend for decades. And since Vyse (who knows of Gonzales' fate) never meets Pedro, the old man will never know.
- The leadup to the ending of Skies of Arcadia has several. Just about every major plot point from Gregorio's appearance on Dangral Island to just before the Air Pirates rally can choke you up.
- Drachma's reason for hunting Rhaknam turns out to be because he killed his son.
Drachma: "They called him...Little Jack." And...those feathers.- The end of Glacia. Especially with the above in mind, realizing that Rhaknam completely turned the other cheek, saving Drachma's life, was quite shocking...only capped by the realization that Drachma had been watching over his former sworn enemy in its dying moments, especially for someone as stubborn as Drachma. This is immediately followed by the most heartrending cry you will ever hear, and Rhaknam crying a single tear upon hearing Drachma say "I see...it's time for you to go. Don't worry. I'm here for you."
- The credits are notable as they tell the fates of all the members of Vyse's crew after the journey. Drachma's ending doubles as a Tear Jerker and Heartwarming as he dies of old age just six months after the ending, but happily as a fisherman.
- Ramirez' Fallen Hero Start of Darkness. There's no exonerating him from the evil things he did, but the fact that his Despair Event Horizon turned him from proto-Vyse to the monstrous zealot we meet in the present is saddening, to say nothing of how his actions have hurt Fina.
