After Sidney and Vaughn survive the crash, she learns that the man she has known as Michael Vaughn is under investigation and suspected of being a double agent. She questions whether their business and personal relationship over the years had all been a lie. When Sydney discovers that she is pregnant with Vaughn's baby, she is determined to uncover the truth about him. Meanwhile, because of Jack's past betrayal by Irina, he begins to worry that his daughter may suffer the same fate as he did. He will also have to deal with the fact that he will soon become a grandfather - while still learning how to be a dad. Sloane will have to do some soul-searching of his own, as he makes an unholy alliance in his desperate fight to find a cure for Nadia - who is still in a coma. New agents enter the fold and a new organization rears its evil head.