There is no way Rogue will be able to take the emerald from Shadow in a 1 on 1 battle, meaning that Scrouge will personally have to take it from him using the powers of the chaos emeralds he already has. I guess for story sake, I can have shadow actually try and look for the emeralds when...
This is mainly because Shadow will most likely have an emerald with him in order to cast chaos control, so Scrouge would have to take it from him which I think is kinda unavoidable. Then we can have the characters that are a part of team sonic group up and try to get the master emerald due to...
I think that we should start from some time before the Genesis wave when Scrouge is collecting the emeralds. Then you can go through that process and our characters can interact before the thing actually begins.