Here is my take on the DEAL:
I think that Sami makes a deal with EJ not to harm Rafe. Sami tells EJ how Rafe took care of her while she was pregnant with his child and all the good things that Rafe had done for her. She reminds him of the laughing Penguins and how Rafe was knifed by Sami's killer. She tells EJ how she nursed him back to health and how he really protected her. Rafe did so much for her and put his job on the line to protect her. EJ because he loves Samantha will make a deal not to harm Rafe. EJ realizes that Sami is not in love with Rafe and that Rafe poses no threat to him. EJ still loves her so much and he will not do anything to hurt her, he knows the DiMeras have hurt Sami enough this is why she cannot admit her love to him.
Sami does not want Stefano and all the violence. This is why she wants EJ out of the mansion. I think she also tells EJ that Stefano put the hit on her. If she says that it was Stefano's way of getting revenge, so to smooth it over becasue she knows how much EJ loves his father too. She may try to tell him who knows maybe it was Stefano's acting on his threats. Remember when he called them all together to confront them alll about what Marlena had done to him, when he was in that coma. This is my take on the deal.
I am keeping this thought, the deal is Sami saves Rafe!!