Crystal Palace was attacked by the Negamoon Family, led by Prince Diamond, who wanted to get revenge on those who banished him to the Planet Nemesis. Sailor Mercury, Sailor Mars, Sailor Jupiter, and Sailor Venus used their power to protect Crystal Palace, making it invulnerable to any attack, so Diamond send Rubeus and the Negamoon Sisters, and later Emerald, into the past to take over Tokyo to automatically make Crystal Tokyo disappear.
Inside Crystal Palace, Neo Queen Serenity was put to sleep by the evil forces, and encased in a layer of quartz by the Sailor Scouts to protect her. The Sailor Scouts of the past, along with Tuxedo Mask, Luna, and Artemis, entered Crystal Palace with Rini to hear the legend of the Negamoon. Later, Emerald asked Wiseman for power to destroy Crystal Palace, and he tricked her with a dark crown, turning her into a dragon. She then attacked Crystal Palace, but was unable to destroy it, and was destroyed by Sailor Moon.
- Crystal Palace shares its name with the seventh major level on the Nintendo 64 game Paper Mario, as well as a battle stage on the game Bomberman 64: The Second Attack.