Yes, Rafe is Sami's husband, and therefore Will's step-father (also his girlfriend, Gabi's brother). Sami has two kids with EJ DiMera, son of Stefano and criminal mastermind in training, and he was less than thrilled when Sami married former FBI agent and current cop, Rafe Hernandez; he didn't want Rafe anywhere near his kids, and I think he kind of wanted to fuck with Sami too. Rafe was in some kind of accident, and EJ took the opportunity to replace him with a double, who was a real scum bucket. Sami was kind of going crazy for a while, not understanding what happened to the wonderful man she married and how he'd turned into this horrible person, and she kept trying to make her marriage work, but of course it wasn't happening because the man she was with wasn't actually her husband.

Right now, EJ and Stefano think the real Rafe is dead, but actually he got away from them and now he and Sami have "the creature" (as they like to call Fake Rafe) locked up in a storage closet somewhere, while Rafe pretends to be Fake Rafe and is trying to get proof that EJ and Stefano were behind it all.

You've really got to love how ridiculous the storylines get on soap operas!