Five months later. Sydney quits the CIA and joins a Black Ops unit called "Authorized Personnel Only" alongside Dixon, Jack, Vaughn and... Sloane whom for limited immunity is co-operating with the APO. Meanwhile, the truth Sydney found out in Wittenberg endangers her relationship with Jack, and eventually she reveals the awful truth to Vaughn: about her father having Irina murdered over a year earlier.

After Sydney and the APO team infiltrates a formal party at the Chinese embassy in India to locate a fugitive arms dealer, named Janos Vak, Rachel is chosen to begin very first solo mission by infiltrating an off-shore oil platform, with com-links from Sydney whose pregnancy now limits her role in missions, to steal some computer software from Janos to gain the location of a new weapon. Meanwhile, Sloan, now back at APO, is in frequent contact with the elusive Gordon Dean who wants him to keep close tabs on APO, leading to Dean sending his lethal right-hand assassin, Kelly Peyton, to recover the computer software before APO does leading to a hand-to-hand fight between Peyton and the field-inexperienced Rachel.