Sydney discovered Vaughn's true identity -- and the fact that she was pregnant. Together, they set out to learn more about a project called Prophet Five that his father worked on in the past. But before they got anywhere, Vaughn met a tragic end.

Sydney contacts an old friend of Vaughn's to avenge his death. Syd, Dixon and Weiss later find Curtis, the man who shot Vaughn and interrogate him. He is kicked out a fifth story window and falls into the water below. He survives and escapes. Syd, Dixon, and Weiss later ambush him on a plan and Syd finds an unusual container in the cargo hold and sees part of a head and a hand. Curtis corners Sydney and she asks him to tell her the information she needs but he rufuses. He pulls on a leaver and a door flies off into the sky and Curtis is sucked along with it. Meanwhile, Weiss battles the decision whether to go work in DC and a newcomer, Thomas "Tom" Grace joins the team after being enlisted by Jack.

Sydney is forced to partner on a mission with new APO agent Thomas Grace. They discover that Rachel Gibson -- a spy suspected of being involved in activities against the U.S. -- has something shockingly in common with Sydney. Meanwhile, Dixon must accompany Sloane, who’s given a 48-hour pass from prison to acquire a possible cure for his daughter, Nadia.

While Sloane awaits the outcome of his sentencing, Sydney's and her baby's lives is put in grave danger when Gordon Dean discovers that Rachel is still alive.

Syd and Tom discover that Renie has stolen the cryo container, and soon find themselves under siege by a group of mercanaries who want the contents of the container. Meanwhile, Sloane takes matters into his own hands to get himself back into APO and continues his quest to find a cure for Nadia.