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Tear Jerker: Skies of Arcadia
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 still chokes this troper up just thinking about them.
Drachma's reason for hunting Rhaknam. "They called him...Little Jack." And...those feathers.
And 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." That's about the point this troper completely breaks down.
Speaking of the credits and the end of Glacia, 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 Crowning Moment of Heartwarming.