It was set as an alternate universe for the first movie, without Rogue and Wolverine meeting the X-Men. The pairing is those two, obviously, and I think there was some sort of testing plot... Not too sure. They end up on the run, Rogue having nightmares and such and Wolvie being all desperately-protective and taking care of her during freakouts (I'm a sucker for it, as out there as it is). At some point they end up staying in a cabin in some northern town (lots of snow) and bad guys track them down... Etc etc. Rogue is a very weak character in this fic. I believe that they finally associated with the X-Men at the end of the fic, but it's been so long since I read it that I can't really say for certain.
I spent a good amount of time searching for it on the website, but sadly to no avail. Perhaps it was moved, or is just stuck somewhere beyond my search parameters, but I'm hoping that it's still out there somewhere and that someone will be able to help me find it.