They thought they had defeated Dr. Robotnik for good. But it seems Snively, in an act of desperation, has brought a NEW Robotnik from another world, this one calling himself Dr. Eggman.
Now Sonic will have to find and reform the Freedom Fighters to battle this new, overly jovial and energetic Eggman in his "game".
Wait, wait, wait...how would he be able to go back and harvest the same Robo Sonic mk 1? If he went back to the past wouldn't he cause a time paradox by taking the parts before he went back in time in the first place? Thus, the parts wouldn't be there the first time he came up with the idea to repair himself and he'd die? Wouldn't this also apply to Metal Sonic? If he repaired himself, he'd also create a paradox where he couldn't go back in time as he was already repaired.
...Unless this runs on alternate timelines and the only thing they can do is go back to the past, return to the present and then, go back a bit further creating an alternate timeline. I've never played Sonic CD so I'm probably over thinking this.