Board Thread:General Discussion/@comment-24108393-20131205024008/@comment-477304-20131205175530

Perhaps he was offered a position at GUN by the Commander by ways of an apology for his actions earlier.

As for the truth about Shadow post SA2, if the fight between Devil Doom and Shadow last too long, Eggman will confess that he rescued Shadow after he fell to earth, and confirms that he is the real Shadow.