EJ and Sami had no choice but to go on the run to clear EJ's name however an explosion happened, Sami saved Ej from the Salem cops ready to shoot him, the a big explosion happened in Salem, Sami almost fell to her death but EJ is able to save her with some help from will. EJ and Sami go to a safe house that belong to Stefano, EJ and Sami get closer, they end up kissing, however EJ had to find Ian McAllister to confront him, but EJ walk right into a trap set. EJ was Held captive By Ian and Came face to face with Stefano. Ian reveal that Stefano and EJ are in fact, biological father and son. Later EJ got free and took down Ian, afterward EJ told Stefano off and that he want nothing to do with him. EJ go back to the safe house only to find Sami with Rafe who arrested both EJ and Sami, however later EJ and Sami would get out of jail. In August 2012, EJ and Sami the two give in to their feelings by kissing, but EJ is discouraged when Sami reveals that she doesn't want to jump into things and want to focus on her work and kids. Sami decides to give EJ a chance, however Rafe came back into the picture and Sami's life as she begins interacting with him. Rafe tells Sami that EJ no good for her and kisses Sami what cause her to end things with EJ. EJ become angry and confront Rafe, EJ head butt Rafe and two ended up get into a fight, however John and Lucas break up it, EJ decide to get back at Rafe, not just to win Sami back but also to prove that EJ was the father of Nicole's baby. EJ find out from Chad, that Rafe's sister, Gabi was behind Melanie's kidnapping, EJ use this to blackmail Rafe an stay away from Sami, Rafe lets EJ be with Sami, but Sami learns the truth from Chad and get mad at EJ and reunites with Rafe. However EJ got proof, he was the father of Nicole's child but came to find out his son is dead. EJ is heart broken and grief over the death of his son. However EJ get Nicole to confession that Rafe wasn't the father and the baby was theirs child.