The stage where the battle takes place on consists of two long platforms and a large circular platform, each separated by a huge gap which can be crossed via Jump Panels or Formation-specific gimmicks. Primarily, the player must keep up with the Egg Emperor, who will move forward along the stage, attacking the player along the way. Various enemies will also spawn on the platforms (depending on which team is used). The weak spot of the Egg Emperor is the glowing hole on its chest. If the weak spot is attacked, it will put up its shield for defense, although it can be destroyed with enough attacks. It is important to not get too close to the Egg Emperor, especially if the player is launched into the air, as they may touch the Egg Emperor in mid-flight, take damage and most likely fall into the bottomless pit below. The Egg Emperor uses three different attacks:
It slices its lance through the air, creating arc-shaped waves of energy in different orientations which can damage the player.
It launches several homing rockets at the player. These can be destroyed by the player.
It charges at the player if they are too far away from the Egg Emperor. Though its charge is unstoppable, the player can avoid taking damage by performing Fire Combination in Power Formation or a Rocket Accel in Speed Formation with perfect timing.
In front of the player's starting position on the first platform are three Power Cores to collect. After the first platform, the player may switch to the Fly character to fly up to a Dash Ring to receive a yellow Power Core (alternatively, it can also be acquired if the player is in Power Formation and approaches the Jump Panel from as close to the center). At the end of the second platform, there is a Power Gong between two Jump Panels which may be used to receive a red Power Core.
Once on the large circular platform, the Egg Emperor will stay in the center and attack the player from there, although this leaves it vulnerable to the player's attacks. Here, spawning enemies and Egg Fleet cannons will also be present to distract the player.
After a while, the Egg Emperor will fly towards the next stretch of pathway. From there, the player will may use the Pole to receive a blue Power Core. From then on, the level layout loops back to the beginning. As such, just repeat the above steps until the battle is over.
"Hmmm! Enough of this! Sonic! Tails! Knuckles! / Shadow! Rouge! Omega! / Amy! Cream! Big! / Espio! Charmy! Vector! Time to meet your maker!" - Egg Emperor before the cutscene ends.
"I'll show you what real evil is!" - Egg Emperor introduction.
"Take this!" - When Egg Emperor is slicing spears.
"Ha ha ha!" - When Egg Emperor is launching missiles.
"Charge!" - When Egg Emperor is charging at the player's team.
"It's not over yet, troublesome fools!" - After being damaged several times.
"I won't go down that easy!" - When close to defeat.
"Defeated! Impossible! Nooooooooo!" - When Egg Emperor is defeated.
In Sonic X, the Egg Fort II transforms into the Egg Emperor called the "Eggsterminator" in the 4Kids dub. The reason the name was changed was likely to avoid confusion with the Egg Emperor of Sonic Heroes.
Hitting the weak spot on Egg Emperor with Thunder Shoot without stopping is the best way to get an A rank because it will temporarily paralyze and deal damage to the mecha.
In the cutscene before you battle the Egg Emperor, Eggman says everyone's name in formation order (Speed, Flight, then Power).
This is the boss of the Modern Era in the 3DS version of Sonic Generations, which is considered odd since, in the console version of Sonic Generations, Sonic Heroes is categorized as a Dreamcast Era game.