TheDoctor
Member
You mean like Sonic Rush Adventure, because the Extra Boss in Colors DS was literally shoe-horned into the story just for the sake of having a Super Sonic boss fight.
In Sonic Rush Adventure though, where the Extra Boss is you fighting a metal wizard controlled by the Eggmen, the whole existence of the latter is subtly spoilered as you progress throughout the story, from Whisker's general design to him saying after his boss fight "If I don't bring this plunder back... Then ye shall all know his wrath, savvy?", explaining that he was working for someone else.
Well, the Sonic Colors DS storyline follows the Wii version storyline, unless you take the unlockable missions storyline, where Sonic, Shadow, and Omega discover a console in (I think it was Astroid Coaster?) and discover a project Eggman was working on known as project mother. At the unlockable ending we see he meant the Nega Mother Wisp which is the final boss for Super Sonic.