Episode 89 of "Alias"
s05e01 Prophet Five

In the season premiere episode, after learning that the man she has known as Michael Vaughn is under investigation and suspected of being a double agent, Sydney begins to question whether their business and personal relationship over the years had all been a lie. When she discovers that she's pregnant with Vaughn's baby, she becomes 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 that he did. This season, new agents will be introduced and a nefarious organization will come to light in Sydney's life as she fights to protect her unborn child -- all the while traveling incognito, outsmarting the bad guys and keeping the world safe. - description from ABC.com