After a ferocious hand-to-hand fight left Sydney on the floor, unconscious, she awakens to find boyfriend Vaughn waiting for her at a safe house. According to Vaughn, Sydney has been missing for over two years, and he is wearing a wedding ring. Syd must now adjusting to a world that seems upside-down. Will is in the witness protection program; Irina is on the run; Jack is being held in a federal detention facility; Dixon is now director of the division; evil Sloane is now the head of an international relief organization. The main thrust revolves around a new CIA threat, the Covenant.