Spoilers are unmarked
- UrSu (the Master of the Mystics) dies of old age after sending Jen on his quest to restore the Crystal before the new Great Conjunction.
- Gelflings were hunted down to extinction by the Garthim as shown in the childhood memories Jen and Kira share.
- The peaceful and party-loving Podlings being captured by the Garthim and being reduced to slavery by the Skeksis. Making it even worse, Kira attempts to console Jen during his Heroic BSoD after they escape from the raid by saying, "The Garthim have always come." For her and her adopted family, these raids are an inescapable fact of life.
- One of the brave Landstriders who carried Jen and Kira to the castle dies dragged off a cliff by a Garthim, and the other gets overwhelmed and killed by the remaining bunch of Garthim.
- UrTih (the Mystic Alchemist) instantly combusts and vanishes from existence when his Skeksis counterpart, skekTek the Scientist, falls into the fiery pit beneath the Dark Crystal as a result of the laboratory animals' revolt Kira triggered to free herself from the life essence-draining device of the Skeksis.
- Kira's death. It's an in-story one too, for Jen, although the bright light of the Conjunction probably contributed as well. Turns to Tears of Joy when she is restored.
- The end of the film if you think about it. Sure, the urSkeks return to their own world, leaving Jen and Kira to "make [their] world in [the Crystal's] light," but the damage the Skeksis have caused is done; for now, Jen and Kira remain the sole survivors of their race, and have to live forever with the knowledge that this is because of their extermination at the hands of the Skeksis. As for Thra itself, it will take years (if ever) for it to fully recover from the era of darkening caused by the Skeksis' malevolent rule.