With the destruction of Robotropolis, Dr. Eggman relocated his operations to the abandoned city of Old Megaopolis and began construction of a new artifical shell. Learning what Eggman was up to, the President of Station Square dispatched Rouge the Bat to deal with the situation but was captured. The President then sought out the help of Sonic the Hedgehog and Bunnie Rabbot to complete the mission and rescue her.
During Sonic's one year absence Eggman expanded his territory and effectively created the Eggman Empire, with New Megaopolis as its capital ciy. New Megaopolis was the location of Dr. Eggman's Infiltrator factory. Learning of its location, the Knothole Freedom Fighters travelled to the city, infiltrated the factory and destroyed it, along with the Infiltrators.
After being captured by Eggman, Knuckles, who had recently become Enerjak, destroyed a large portion of the city when he escaped from the Egg Grape Chambers. He proceeded to lay waste to the entire city destroying ninety precent of Eggman's ground forces and desimated the entire Egg Fleet.
The Eggman Empire
Dark Egg Legion
The Iron Dominion
The Egg Grape Chamber