How 'bout taking place right after Fusion (Which is apparently at the end of the story)? Samus is running away from the GF, and lands on the ruins of an ancient civilization. (Maybe Chozo. Did they ever get to space?) There, stuff happensm and hilarity ensues.

Of course, someone already did the Metroid Fancomic thing, and it was pretty damn good. And it was scarily similar to Prime 3: Corruption. (It was started before they mentioned any information of it.)