Emily went AWOL to go after Doyle. Team figured it out and tried to track her down. Doyle got to her first, tortured her for a bit. We found out she was engaged to Doyle, and that Doyle had a son from a previous relationship who he wanted Emily to raise so he could be an IRA soilder like Dad. Emily would not do it. She staged the boy's death to get him out, and let Doyle think he had been killed. Team busts in and resuces her, but she was critically hurt. They get told she didn't make it, but only JJ knows she went underground.