I think it might just be one that takes place shortly after the original. I know that the comics continue on the story, and I've even read the first few comics, but I think they might try and place something in between the first season ending and the comics starting. Or, they might even go for something in the middle of the comics. I guess it's a pretty broad area for them.
It's nice that they opted to stick with Bigby though and went with The Wolf Among Us 2, rather than a series more related to the Fables name itself. I can't remember for sure, but I don't think Bigby was necessarily the protagonist of the comics, although I'm sure he was a prominent figure. I'd have to check back on that. But there could have been a chance they opted for another fairy tale character instead. But I gotta love the Detective Noir that comes with Bigby.