- Home World: 4Chan City
- Owner: Adolf Hitler
The Red Gem is always the final gem collected in the adventure. It's unknown what kind of abilities it contained since Hitler surrendered it before his battle with the Unification Squad. It was restored after Link and Zelda defeated Siobhan and Purin.
- Home World: Koridai
- Owner: Siobhan
The Orange Gem was once in the Book of Koridai before its destruction. According to Siobhan, it could restore life to its bearer or send people to The Pit. It was restored by unknown reasons by Gaspra.
- Home World: Gamelon
- Owner: Master Purin
The Yellow Gem was hidden within the Wand of Gamelon. Purin used it to constantly switch bodies to keep himself from dying. It can also imprison people in The Pit. It was restored by unknown reasons by Gaspra.
The Green Gem was hidden in the Ghost Stone Scanty and Kneesocks used in their Ghost Factory. When Panty and Stocking destroyed the stone and the school, the gem appeared from the strong energies gathered. It was later restored after Corset and the Ultimate Ghost were defeated.
- Home World: Real World
- Owner: I.M. Meen
The Blue Gem was in I.M. Meen's possession after the first attempt to summon the gods. It's unknown what abilities it had since he never used it. It was later restored after Big Red was defeated.
- Home World: Gensokyo
- Owner: Yukari Yakumo
The Indigo Gem has always been in Yukari's possession, though she never admitted to having it. She gave it to the Unification Squad after they nearly died at the hands of Rumia. It was later restored after Yukari was defeated.
- Home World: Hyrule
- Owner: Gaspra
The Violet Gem was hidden away in Tolemac by Gaspra after Zelda brought the Age of Lightness. He returned it to her after the gems of Daten City, Real World, and Gensokyo were gathered. It was later restored by Gaspra by unknown reasons.
- The Gems of the World could either be based off the Chaos Emeralds from the "Sonic the Hedgehog" series or the Rainbow Crystals from the "Sailor Moon" anime. The sprites for them are based off the latter.
- If the gems are destroyed after their uses, it's unknown how they were restored the first time around.
- After the True Darkness awakened, Chip manages to use the gems one final time to restore everyone's confidence in themselves.