Quoting this thread from the SEGA forums.
"Okay, I'm just gonna copy pasta atm.
According to a Japanese friend, the manga of Sonic Generations says that Sonic Generations takes place 5 years after the end of Sonic Colors, and these last few years have been peaceful. Sonic is celebrating his 20th birthday with Tails and Amy when chaos begins to ensue the world and he finds himself in the past with himself. However, this is not the most interesting bit, but something strongly hinted at he and I were talking about.
Okay, you know at the end of Sonic Colors, when Eggman gets sucked up into the giant exploding amusement park and then we see him drifting through space later saying he already has his revenge planned out? APPARENTLY Eggman hasn't been seen since then. It also seems hinted that somethings changed in the past, something is causing things to go wrong with the timeline, as well as everything being eaten and turned into nothing. This is just a theory piecing everything together, but it's plausible that the Time Eater is a creation of Eggman's but before he had a chance to put it to use, it erased Eggman from the timeline OR Eggman somehow became one with the Time Eater. This sounds crazy, I know, but something that seemed weird in the manga was that the Time Eater seemed to be targeting Sonic, and though only a brief glimpse is caught of it, Sonic seems startled to see it, to the point he does the Japanese equivilent of, "It's..."
So crazy jackpot theory time, somehow in someway Eggman is the Time Eater, but not exactly. My current theory rests that the Time Eater removed Eggman from the timeline or their somehow interchangeable, which might also explain why Eggman isn't in any sort of new form himself. All the other main Sonic characters have been tossed around the time tables, except for those who are directly influenced or sided with Eggman. So completely rumor and theory, and I want some people to pick up the manga and confirm as I haven't seen it, only told bits and pieces and his English isn't the best, but currently placing my bets on it being a creation of Eggman and possibly even part of it IS Eggman. The things seems to eat Time, and my guess is that it gains influence over what it eats and if the only thing it's eaten up until this point is Eggman...
My iPod is stupid and won't let me quote right.
Something to note though, the manga adaptions tend to be different from the actual game, but some events do stay true to source material. This is strictly a rumor, so take with a gigantic handful of salt.
I think it might be fake, but it sounds okay, but kinda "meh."
What do you think?