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The Egg Bosses serve as commanders to various Egg Army factions that are stationed in different locations around Mobius. Like the Grandmasters before them, they are forced to work for the Eggman Empire and usually anatagonize a region's local Freedom Fighters. Their mechanical equivalents are the Horde Commanders of the Badnik Horde.
- Abyss the Squid - Southen Oceans Egg Boss
- Akhlut the Orca - Northern Oceans Egg Boss
- Axel the Water Buffalo - Efrika Egg Boss
- Conquering Storm - Yurashia Egg Boss
- Clove - Northamer Egg Boss
- Cassia - Northamer Sub-Egg Boss
- Battle Lord Kukku XV - Egg Boss of the skies
- Maw the Thylacine - Tralius Egg Boss
- Mordred Hood - Eurish Egg Boss
- Nephthys the Vulture - Midesta Egg Boss
- Thunderbolt - Soumerca Egg Boss
- Tundra the Walrus - Artika Egg Boss
- Wendy Naugus