So, Eggman is obviously dead by Silver and Eggman Nega's time in the future, most likely of old age as he always survives his fights with Sonic.
But, is there any particular reason why Eggman didn't transplant his brain into a robot like his Dragonball Z counterpart, Dr. Gero? Or does he do that and end up being killed by Sonic? I know it's completely unknown, but it gives us something to speculate about