When the battle starts, Sonic is running on the outer ring (the one around the central arena) with the Egg Emperor flying ahead of him. In order to deal damage, the player has to attack the Egg Emperor's torso. During this turn, the Egg Emperor will throw vertical and horizontal energy slashes at the player. The energy slashes fired by the Egg Emperor cannot hurt the player if they are using the Boost; instead, they cancel out the move and the player's momentum. At the same time, the cannons on the central arena will fire homing missiles at the player. These homing missiles can be destroyed with a Homing Attack or the Boost, which will in turn fill up the Boost Gauge.
After inflicting some damage on the Egg Emperor, it will fly toward the central arena. Sonic, however, will follow it to the said arena automatically using his Air Boost (without depleting energy from the Boost Gauge). In this arena, the player can run around the area and hide behind the cannons while the Egg Emperor is throwing its attacks at Sonic from the center of the arena. In order to lure the Egg Emperor into coming to the player's location, the player has to use the Homing Attack twice on one of the cannons to make it fire its homing missile at the Egg Emperor (this process also gives the Boost Gauge some energy). When this is done, the Egg Emperor will fly up to the cannon the player used and destroy it. At that moment, the player has to launch a quick attack on it. Whether the player succeeds or loses their chance, the Egg Emperor will return to its position in the center of the arena immediately afterward, and the player will have to repeat this pattern again. After some time has passed, the Egg Emperor will move back to the outer ring, and so will Sonic. When this is done, the player has to once again dodge his slashes and missiles, and proceed forward to attack his torso.
Until the Egg Emperor's Health Gauge falls to one percent, it will keep switching the battleground between the two aforementioned areas. When its Health Gauge falls to one percent however, it will immediately charge to the central arena. This time around however, its will launch a barrage of energy slashes while aiming them at the player, and by extension, the cannons. In order to attack the Egg Emperor one final time, the player must wait until the Egg Emperor charges at Sonic. When this happens, use the Homing Attack or the Air Boost directly at its torso.
It takes eight hits in order to defeat the Egg Emperor.
- 1-Ring Boss: Defeat Egg Emperor in 6:00.00 with 1 Ring!
- The Egg Emperor is piloted by Dr. Eggman, as opposed to Neo Metal Sonic who piloted it in Sonic Heroes.
- This level is the boss for the Modern Era, despite Seaside Hill (another level from Sonic Heroes) being a level in the Dreamcast Era on the Console version.
- If the player tries to leave the area (moving left), the Egg Emperor will do a forward slash that is unavoidable that will instantly kill the player if they do not have any rings.
- The Egg Emperor is also in a slightly different color compared to its appearance in Sonic Heroes.