The last time I remember seeing it was awhile ago, and it was WIP. It takes place in something like the colonial times, or the Salem witch trails. I think people generally knew about werewolves, though they lived pretty much separately from human society (that might have been because the Argents live in town). Kate and Derek were involved before she killed his family, and she ended up having Isaac. She didn't want a werewolf child but couldn't kill him and be a kinslayer, so she left him in the woods to die. But Stiles, who lived on the fringes of society since he was a hedgewitch, saw it and took Isaac in and raised and protected him. Not too many years later, someone has figured out that a werewolf lived there, so Stiles and Isaac decided to flee and try to find Isaac's birth father, who probably lived with a pack nearby.
Anyone know this one? They were updating pretty regularly so I didn't save the link and now I can't find it. I'm dying to read it again, or see if I missed updates!
Edit: Found!
http://archiveofourown.org/works/522733?view_full_work=true