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.
- The 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.
- One of the brave Landstriders who carried Jen and Kira to the castle dies falling off a cliff along with 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.