In "Eye of the Storm", Thorn's raw and tearful breakdown when she learns Gran'ma Ben kept secrets from her, about how her parents were killed by rat creatures and how she's royalty. It's such an intense moment that not only marks Thorn's loss of innocence, but also her broken trust in Gran'ma Ben.
Any scene involving Gran'ma Ben or Lucius late in the story when they don't know where the other is.
In "Dragonslayer", Lucius and Fone Bone find Thorn in her room sitting silently on her bed. When Lucius calls to her, all Thorn can do is whimper "Oh, Mister Down..." and collapse into tears in his arms.
Jonathan's deathbed scene.
What makes it even sadder is that Ted the bug is blissfully unaware that he may have borne witness to Jonathan's last moments.
Lucius's backstory of almost (but not quite) getting married is sad enough on paper. But even sadder is when he shares the entire context of how his love life went horribly wrong. When he was younger, he knew Briar and Rose when they were the two most beautiful women in the valley. He describes that Rose was a kindly woman while Briar (well) was "grown-up in a woman's way". As he so sadly puts it, he chose the wrong one. To top it off, it's all told to the illustration of a downcast Princess Rose leaving in defeat as her sister shoots her a sadistic smile at having hurt her, while young Lucius watches on with an expression that second-guesses his choice.
The wasteland state the valley is left in after the eruption is an ashen sight to behold
Fone Bone fearing for Thorn's life when she reveals her plan to go after the Crown of Horns in order to destroy the Locust, but might kill her too because of the piece inside her, and trying to talk her out of to the point of tears when Thorn doesn't deny it.
Fone Bone: It DOES mean that! PROMISE ME YOU WON'T DO IT! (crying) THORN! THORN — PROMISE ME PLEASE!
Thorn seeing her dead mother in her dreams. She sadly notes to Fone Bone that its the only time she's ever seen her face.
Fone Bone saying goodbye to everyone, particularly Thorn.
Thorn: I packed you a little basket of biscuits and honey. I saved it until now because...I was hoping you'd change your mind. Fone Bone: Thorn... Thorn: So much has changed since that day we met at the hot springs, and you walked out of the woods with your hat on fire...but not everything changes. Remember me when you're back in Boneville. Fone Bone:(Hugs her)oh, I...I'll never forget you, Thorn. I don't think I could.
If it's any indication, even Phoney seems saddened.
For context, Phoney at this point is still under the impression he's about to ride back home with a big chest of treasure. Everything is going his way, so you'd think he'd have no reason to be down. And yet, he's notably somber in this scene.
The flashback showing the dragons fighting the Lord of Locusts aka Mim, their beloved queen.
Even sadder when you learn in "Tall Tales" that the Great Red Dragon (who was amongst the dragons that fought her) is in fact Mim's son.
Lucius' funeral.
Rose's very last words to Lucius in "Old Man's Cave": "Good-Bye, Lucius."
