Having acquired six of the seven Chaos Emeralds, and taken Christopher Thorndyke Chaos Emerald from his robot, E-77 Lucky. Both Sonic and G.U.N.'s Beetle robots tried to stop Eggman, but Eggman used the six Chaos Emeralds to transform the Egg Fort 2 into the Eggsterminator.
The Eggsterminator destroyed the government robots and powered by the Chaos Emeralds, could move faster and attack stronger than Sonic. However, all the power sent it out of control, causing it to attack Sonic and co. without hesitation and glow an orange color. Fortunately, Chris was able to break free from the Eggsterminator, grab the six Chaos Emeralds (badly burned by the Emeralds' energy being in use), and jump out of a window. Chris was rescued by Rouge the Bat, but Sonic and all seven Chaos Emeralds fell into the sea, where Sonic was transformed into Super Sonic. In this transformation, Super Sonic was able to destroy the Eggsterminator, ramming it multiple times.
- The Egg Emperor was named Eggsterminator in the 4Kids dub, and the name may have been changed to avoid confusing it with the Egg Emperor from Sonic Heroes.