Sonic and his friends went to future and discovered that Sonic had got children from each of the main Sonic girls.
The problem is that some of them had joined the side of Eggman, no more a human but a coscience inside a huge computer. Skyscream is one of them. He has killed both his mother and father and then he has becomed the second in command after Eggman.
But, as Sonic and the others soon discover, the truth is more than meets the eye. Infact Skyscream was not satisfied with his role of number 2 and so he has secretely erased Eggman's coscience from the computer and has taken control of it, pretending to be the doctor himself and tricking Eggman's fellows too.