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Tear Jerker: Spider Riders
Sparkle's reaction to Grasshop's betrayal in "Grasshop's Misfortunes", Sparkle keeps giving Grasshop a sad and hurt look. It's so sad that Grasshop can't even bring himself to look her in the eye. It's no wonder Grasshop wanted so badly to make things up to her later on that he did a Heel-Face Turn for real.
Sparkle: (confused) Why are you doing this Uncle?
Grasshop: (Grasshop looks at Sparkle but turns away when he finds he can't look at her) *I wish she wouldn't look at me like that! She is my enemy! So why should I care how she feels?*
Poor Grasshop in "Spies and Lies", having to chose between betraying the Spider Riders or never seeing his wife and children again. The poor guy.
When Stags appeared to commit suicide after Hunter had beaten him in single combat. Like Hunter, I wanted to try and grab him before he fell.
Watching poor Beerain collapse and cry in despair at the end of "Fly No Longer". That scene alone is enough to make just about anyone feel sorry for her.
That's nothing compared to the way Buguese treated her when she finally did manage to catch up to him. You could tell that his being forced to disavow her in order to stay in Mantid's good graces was eating him away inside.
Watching everyones reactions in episode 45, to losing sight of Hunter and Shadow after their fall from the bridge in the Labyrinth. Corona keeps shouting into her Manacle while hoping for a response. Magma is furious and rages, Lumen just sits and sulks, while a devastated Grasshop tries to comfort the crying Sparkle.
In "Mantid's Trap", when asked why he didn't step up against Mantid sooner. Quake reveals that many of his fellow Spider Riders died during their last encounter, and he didn't want to repeat the experience.
The apparent death of Buguese near the end of the series. Even if you loathed him up to that point. You can't help but be impressed with his determination.
Hunter: Goodbye Buguese...
Even though he'd been a complete douchebag for the entire series, Mantid's story of the loss of his wife really gets you.