How far is Rafe going to go to cover up the fact that Sami shot E.J.?
As far as he needs to. In Rafe’s mind, what she did was justifiable. The only thing that he has reservations about is that in reality [E.J.] is the father of these children and obviously that’s a difficult thing but the guy is so successful at manipulating people and driving them crazy that in Rafe’s mind he took what was already an unstable woman i.e. Sami and drove her to a point where what she did was rational, after he had kidnapped one of her children then threatened that he was going to take the other. What mother wouldn’t lose it? It’s not like she went there pre-meditated to shoot him. She went there and he was passed out with a gun, so how convenient. He’ll do what he can to protect her.