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Demento's death in the Fire Orb saga. The music accompanying it only doubles the tear factor.
The prequel quest to 2011 Mogloween. Even though it doubles as horrific, the only survivors shown are kids and we don't know what happened to them. They were supposedly left behind. Andy definitely survived, but he was bitten and is a semi-transformed Zardbie. Unfortunately, anything he bites or kisses (or that kisses him) is... well, he DOES carry the virus, even if he's not affected by it.
Going to Falconreach after the timeskip that leads to book three. Seeing Aria and Ash all grown up, and knowing you didn't get to see any of it...and all of the displaced magical creatures...
Remember the dragon from the first chapter intro? At the chapter three intro, as you stand on the cliff, a red dragon in chains flies by, then gets shot down and presumably killed by the Rose members. What are the chances it's the same one...?
The Duel. Even though everyone already knows how it ends, just watching the whole thing fall apart is horrible. And it's even worse once you know the conclusion to Chapter 2.
For the Atealan quest armors, you must complete a challenge to acquire each one. For the Cryptic, you must face your fears and regrets. You fight Drakath, afraid he might come back, stronger than ever. You fight Warlic, no longer trusting your closest friend after the events of Chapter 2. And...yourself. You no longer trust yourself to protect anyone, you couldn't save those who died. And it's kinda sad to see our cheerful hero/heroine literally beating themselves up over that they couldn't save people! You come to terms with it after the fight but, well, it's weird seeing Dragonfable no longer be a kids' game.
The Soulless cutscene in Part Two of the Ravenloss Saga, in which you find out someone close to Tomix is lying comatose and Tomix talks to him as if he were awake and cries
The intro to Chapter 3 where your Dragon tries to rescue The Hero from their ice crystal. Such things involve begging and trying to claw his way inside to rescue you.
The Tomix Saga Finale. Even the devs had tears of sadness! The forum goers were all reduced to blubbering wrecks!
Heck, even the characters were crying! Even Yashta, who has never shown any sign of emotion aside from boredom and satisfaction, shed a tear! Then there's the Epilogue.