The Egg Fortress, true to its name, is a large egg-shaped superstructure with smaller egg sub-structures connected to it. It served as Robotnik's primary base of operations for several issues and it was there that many of the doctor's most devious creations were built, including the super-Trooper Predicto and the Brotherhood of Metallix.
At an unknown point in time, Robotnik abandoned the Egg Fortress for unspecified reasons and transferred the seat of power to Citadel Robotnik in the Metropolis Zone. The fortress was still active, however, becoming base of operations for the Brotherhood of Metallix. From there, the Brotherhood hatched their plan to hijack the Omni-Viewer and create their own copy of it, thereby gaining the power to travel through time and space. Knuckles the Echidna and new friends, the Chaotix Crew, ventured here to retrieve Omni and put an end to the Metallixes, with Mighty the Armadillo raising the alarm by punching his way in. A lone Metallix was sent to tackle them, almost succeeding in defeating them until Knuckles disabled it for a while. The team were soon betrayed by Nack the Weasel, leading the heroes right into "the lion's den". When Nack himself was betrayed, a final conflict with the Metallixes led to Knuckles using Nack's disruptor gun to seemingly wipe them all out. After Chaotix abandoned the base, a back-up system activated which brought the robots back to "life". Without any interruption, the Egg Fortress was once more a secret base.
The Metallixes also brought their creator Grimer to the Egg Fortress and forced him to build the Alpha Device. Upon discovering that his own creations had failed him, Robotnik enlisted Sonic to venture to the Egg Fortress and rescue his scientist. After searching the acres of the base, Sonic eventually located the Emperor Metallix moments before they achieved their goals. Sonic stole the Alpha Device and defeated the remaining mooks, but relented when the Emperor threatened to crush Grimer. After this moment of weakness, the Metallixes abandoned the Egg Fortress and travelled to the Miracle Planet. The fortress has not been used since and was presumably destroyed along with the entire Special Zone in Issue 233 (of Sonic the Comic Online).