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Tear Jerker: Saber Rider and the Star Sheriffs
"Trista... Maybe in another lifetime... you and I will be friends. Real friends". Poor, poor April
The I Have Your Wife episode where the team sees Commander Eagle used as a hostage and placed inside the mecha of the week. It's really sad to see Eagle urge them to destroy the mecha even when it will kill him... and they do since there's no other way to stop them. In a subversion, he was never there: it was another trap of Jesse.
Also, the chapter when Colt tells his backstory to his girlfriend Robin. When he saw his parents die as the Vapor Beings destroyed their shuttle.