This is based on opinion. Please don't list it on a work's trope example list.
Tear Jerker / Stellvia of the Universe
Stellvia takes place in a world where war is such a distant memory that most of the teenage main characters don't even know what it is. This makes it all the more tragic when a confrontation with alien spacecraft turns suddenly, devastatingly deadly. The slow, haunting rendition of the opening theme playing in the background—a more upbeat version of which previously played in-show during moments of triumph—doesn't help. Neither does finding out later that the aliens were actually trying to help humanity, and only killed in self-defense. If the Foundations hadn't fired first, no one would have died.
The entire last episode, but especially when Stellvia goes into the fracture.