The Eggdome is a huge egg-shaped dome in New Megaopolis made for emergencies and was formerly the main base for Dr. Eggman and the Dark Egg Legion after Enerjak destroyed most of the city. It is now used by Snively Robotnik and the Iron Queen after Sonic the Hedgehog drove Eggman into insanity due to constantly defeating him. It is perfectly suited for housing about a hundred soldiers and also has all the necessary equipment for Eggman to build and test his machines.
After Enerjak's destruction of New Megaopolis and all his Badnik forces, Eggman was forced to retreat into the Eggdome for cover, but left a short while later in response to Lien-Da who contacted him for an alliance to replace his troops in return for him restoring their cybernetics. Eggman agreed, but Lien-Da was not made Grandmaster as she hoped. That position had already been filled by Dimitri as he proposed an alliance to Eggman first, therefore, winning the rank. Eggman also made sure they didn't rebel against him by placing bombs in the cybernetics he provided them with.
When Sonic the Hedgehog and the Chaotix were attempting to destroy Eggman's communications tower, the D.E.L. had to rush out of the Eggdome and into the field of battle under the command of Lien-Da and later Dimitri. They lost and the tower was destroyed, stopping Eggman from contacting half the continent, just as Dimitri hoped.
Eggman later created a new robot in the Eggdome, a new Metal Sonic that he could control and even speak through, to take down Sonic and the Freedom Fighters at Freedom HQ, only to find that it had been taken over by King Scourge the Hedgehog and his Suppression Squad. Scourge told him that he should leave, but Eggman decided to take out his wrath on Scourge instead. During the battle, Sonic arrived and it turned into a three way fight, and soon a two way fight when Metal Scourge arrived and Sonic and Scourge formed a temporary truce. Meanwhile, Dimitri confronted Eggman about why he had not yet made a new army of robots so the Dark Legion would no longer have to work with him and they could return to their lives, but Eggman said that he wanted to use the Echidnas until there were none left and that if Dimitri had any more complaints, he could discuss it with the bombs placed in the D.E.L.'s cybernetics. Later back at Freedom HQ, Metal Sonic and Metal Scourge were destroyed by Sonic, Scourge and the Suppression Squad that was reluctantly used by Scourge.
While Eggman was building one of his next battle machines, the Egg Tarantula, he ordered Snively Robotnik to go away as he was doing nothing but sitting around thinking and not assisting him. After being humiliated by Lien-Da and a Dark Legionnaire, Snively decided to perform a routine maintenance check on the Sub-Bosses as communications were still possible in the Eggdome even after the Chaotix's assault via Egg Network, which allowed Snively to come into contact with a Sub-Boss known as Regina F, who he became romantically attached to and started planning a rebellion with.
Eggman and Snively then set about work on a new Metal Sonic; this time equipped with a SXSU-401 engine that was capable of teleporting through zones instead of the typical STH-25 model. But before Eggman could give it its orders, Metal Sonic teleported away to Sonic's location in Moebius where he was fighting Scourge, causing the doctor to go into a fit of rage. That Metal Sonic was later destroyed by the combined efforts of Shadow the Hedgehog, Blaze the Cat, and Marine the Raccoon.
While Snively was talking to Regina, Eggman ordered him to assist him in testing his latest machine, accidentally calling him by his birth name of Colin in the process due to his rapidly decreasing hold on reality. Snively quickly made jokes about his next invention being something ludicrous like a minnow or rabbit, but he was soon shut up when he that his "uncle" had created a pyrotechnic killing machine called the Egg Phoenix.
The Egg Phoenix was soon put to use when the Freedom Fighters and Chaotix made an assault outside the Eggdome against the Dark Legion. Eggman piloted the Egg Phoenix and almost killed the D.E.L. when trying to fry the Freedom Fighters. Dimitri openly protested to this while talking to Snively in the Eggdome who was watching the battle. He then told Snively that he knew about Regina and his plans and said he'd turn him in to Eggman if he didn't see to it that the Dark Legion was kept safe, but Snively convinced Dimitri to keep his mouth shut by saying that they could both benefit from his and Regina's plan. Soon after, the Egg Phoenix was destroyed and Eggman ordered Snively and Dimitri to round up the Dark Legion for tomorrow's final battle.
The day after the Egg Phoenix's destruction, Dr. Eggman saw to the rooftop launch of his last E-100 series robot, E-123 Omega, on a mission to destroy his old rouge unit, E-102 Gamma (Omega was successful, but ended up rebelling against Eggman in Gamma's stead). Meanwhile, the D.E.L. attempted to defend the Eggdome against the Freedom Fighters' and Chaotix's assault with Lien-Da as acting field leader, ordering them to build a barricade with a hole big enough to let Sonic in, while secretly preparing to put Snively's plan into action. The D.E.L. came through with the aniticipated and wanted results; failure. Lien-Da then ordered the Dark Egg legion to move on to phase two of the plan; retreat in order to let Sonic through for him to go up against Eggman. Sonic made it through alone, due to Eggman preparing a trap with the barricade the D.E.L. built that was perfect for Sonic's spin dash. The D.E.L. saluted Sonic as he rushed passed them to fight Eggman and were then ordered to make sure that the Freedom Fighters and Chaotix were kept at bay until Sonic was sealed in with Eggman in his Egg Tarantula.
Sonic managed to defeat Eggman, however, and Eggman lost his mind. Snively then came in and explained to Sonic and Princess Sally Acorn that he had drove Eggman into insanity by constantly defeating him, despite Eggman's great genius. Snively then told them to return home and celebrate. Once Sonic and the other Freedom Fighters had left, Snively had Eggman imprisoned in a straight jacket and padded cell, while he made his way to the landing bay to greet his sweetheart, the Iron Queen, and her forces who had arrived via derigible.