The Iron Dominion is a gathering of Mobian clans under the command of the Iron King and Iron Queen. Including the Yagyu Ninja clan and others, this group formed in the Dragon Kingdom and fought against Monkey Khan before relocating to New Megaopolis to usurp control from the insane Dr. Eggman. It was formerly a branch of the Eggman Empire, but following the empire's decline it had effectively become it's own government. The Iron King and Queen later usurped the Eggman Empire entirely into the Iron Dominion's domain.
During the Clan Wars, the Iron Queen got involved and killed the leader of the Yagyu Clan, the Bride of Rich Nights. Following this she took the Yagyu Clan as her own vanguard, and due to her powers, the other three clans surrendered to her, making her the Bride of Four Houses. Since then, all four clans have acted as her soldiers.
While the Iron King and Queen served as Sub-Bosses to the Eggman Empire over in the Dragon Kingdom fighting the local resistance there, who were beginning to keep them at bay, the Iron Queen made romantic connections with Snively Robotnik over in New Megaopolis via the Egg Network. After the Iron King and Queen had finally managed to rid most of their oppressors, the leaders of the Iron Dominion, accompanied by the Yagyu Clan and Conquering Storm, arrived at the landing bay of the Eggdome via the Iron Queen's dirigible to usurp the Eggman Empire following Dr. Eggman's recent descent into insanity, and quickly began a search of the city to see if their were any other functioning buildings other than the Eggdome.
Espio the Chameleon
The Yagyu Clan
The Dark Egg Legion