The main antagonists of Season 2 (The Invasion of the Rajita) and are old enemies of the Moon Kingdom/Sailor Senshi.
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- Knight of Cerebus: In a way, their existence marks a game-changer to the YYGDM franchise. Their invasion on Earth sets the stone for epic battles and wars.
- Lizard Folk: They are a race of reptilian aliens, both humanoid and animalistic like.
Kaiser Ghidorah
See Yu Yu Gi Digi Moon Season Trilogy Villains for his page.
The Four Generals
- Expies: To the Shitennou of Sailor Moon.
Kuiiza (OC)note
- The Dragon: To Kaiser Ghidorah.
- Mad Scientist: Shows off a lot of cruel experiments.
Kujiko (OC)note
- The Brute: Focuses on brute force.
Nagah (OC)note
- Dark Chick: The only female of the generals.
- The Dragon: To Gamera in Season 3 (Dawn of Chaos).
- Dragon Ascendant: Will become the new leader of a reformed Rajita after Dawn of Chaos is over.
- HeelFace Turn: Later on in Dawn of Chaos after seeing what Gamera become thanks to Paradais.
Morpheous (OC)note
- HeelFace Turn: After his experiences with the Duelists.
- Official Couple: With Serenity Wheeler.
The Great Leviathan
- Greater-Scope Villain: It's the Rajita's god and where the Orichalcos is alien origin.
The successor of the Rajita. These forces are ones abandoned by Ghidorah for being useless. Nagah raises Ghidorah's successor, Gamera, who would lead the faction. Their main base is hidden in the Digital World, that they improve their experiments for the aliens to have Digimon DNA. Somehow, Gamera forge an alliance with Sailor Charon and The Prophet.
Gamera
See Yu Yu Gi Digi Moon Season Trilogy Villains for his page.
Melancholia (OC) note
- Animal Motifs: Has the DNA of Myotismon.
- Expy: Of Ulquiorra.
- HeelFace Turn: Maybe, after defeated by Sedna.
- The Stoic
Vipris (OC) note
- Expy: Of Nnoitra Jiruga.
Geso (OC)
Blitzkrieg (OC) note
- Animal Motifs: Has the DNA of Dinotigermon.
- Expy: Of Grimmjow.
- HeelFace Turn: Later on.
- The Rival: To Sailor Varuna.
Toad (OC)
- Animal Motifs: Has the DNA of Parasimon.
- Expy: Of Szayel Aporro Granz.
Babbi (OC) note
- Animal Motifs: Has the DNA of Gorillamon.
- The Brute
- Expy: Of Yammy.
Kitoss & Wolk (OC)
- Animal Motifs: Has the DNA of SkullScorpiomon.
- Expies: Of Loly & Menoly, but Kitoss is more evil than Loly.
- Hate Sink: Kitoss is detestable despite being a minor character.
- HeelFace Turn: Wolk.