Compared to how they made him second banana to some other big evil bad guy in most of the other games, what really was the crowning moment of awesome is how he uses Sonic and the gang to defeat Ix, leaving them unable to fight him while they're in the other dimension. He expected them to never return, but he was fine when they came back to see that he had rebuilt in their absence. While Sonic still has the Chaos Emeralds, Eggman appears to have taken over, possibly to the extent that he truly has an Eggman Empire now. In the game continuity, this is about the closest he has ever come to realizing his dreams. This 'plot' starts about halfway through the game.
Eggman: Welcome back, team. You've been gone a long time... might've been better if you hadn't returned. But I was hoping you would.