Department of Special Research gained interest in Sydney's role involving the page 47 and they began their own investigation regarding it. To save herself, Sydney needs to steal 500 year old Rambaldi codes from Vatican to decipher Rambaldi's prophecy. Meanwhile. Sloane gets suspicious that one of the Alliance's members switched sides and is now working with The Man.

While Sloane is desperate to buy few more days for his wife, Will, with a help of Jack, sets up a meeting with his contact "Deepthroat" in Paris. As the luck would have it, Sydney and Dixon will be there at the same time trying to steal a very important document from Khasinau aka "The Man" and his right hand, Mr. Sark, who was just recently in the custody of the SD-6.

Sloane must take a difficult decision in order to get to the Alliance's council. After being captured by Sark, Tippin is tortured by a Taiwanese would-be dentist to extract secrets. Sydney, who has to beware her colleague Dixon, assist her father trying to save Tippin. However, after losing Vaughn when the lab exploded, she is in for a surprise...

Sydney finds herself face-to-face with her long-lost mother, Irina Derevko, whose intentions for her daughter are made chillingly clear. However, Sydney manages to escape and rejoin Jack and Will in their escape from Taiwan. After arriving back in Los Angeles, Sydney continues her search for Vaughn, not knowing if he is dead or alive after being swept away by a wall of water in Taipei. Will's life is forever changed when he learns the truth about SD-6 and Sydney's life as a double agent. Also, Dixon must decide whether or not to inform Sloane of Sydney's suspicious activities. But Jack intervenes and covers for Sydney who later finds Vaughn who helps her try to track down her mother Irina who's searching for a Rimbaldi artifact called 'the Bible.'