Sloane decides to betray Dean when he learns that Nadia's condition will probably not improve. They meet at a race track in Dubai to exchange a network access card which Sydney and Renee stole in Rome, leading to Dean finally being captured. The APO interrogates Dean for information on Prophet Five. Yet another mysterious stranger asks Sloane to eliminate Dean. Meanwhile, Nadia comes out of her coma for a short time after a nameless nurse leaves her room. Under orders from his new Prophet Five contacts, Sloane kills Dean during a routine reboot of the APO's surveillance network, and APO misses its chance to hack the network, but learns Prophet Five is linked to intelligence agencies around the world. At the end, control of Dean's terrorist cell is given to Kelly Peyton.

One month later, with Sydney on maternity leave, she gets forced back into the field when her old enemy, Anna Espinosa, returns after she's secretly sprung from prison by Peyton who gives her a job offer to work for Prophet Five whose leaders have secretly contact with Sloan to get him to set up Sydney in exchange for getting the cure for Nadia. Anna decides that to get at Sydney is that she needs to go through her friends, leading to Anna to abduct Will Tippen. Sydney, along with APO, is forced to try to find Anna and save Will before he's killed unaware that Prophet Five has bigger plans for Syd, to take a sample of her DNA.

While Sydney and the rest of APO try to learn more about Prophet Five and what their plans for Sydney are, Sloane finally acquires a bottle of serum from Prophet Five as a cure for the comatose Nadia. But Sloane becomes distraught when he learns that for it to work, he must stop Nadia's heart for a full 30 seconds. When the proceeder is successful, Jack becomes suspicious about Sloane's possible involvement with Prophet Five, leading him and Nadia to investigate, while the rest of the APO team continues searching for Anna Espinosa, unaware that she has been duplicated by Project Helix to look like Sydney. Meanwhile, Tom travels to France to meet with Renee to look for a fugitive art dealer, named Moritz, whom has the stolen Rimbalid Page 47 artifact, and learn that it's a fake for the real one has with Sloan all this time. Also, Sydney offers Renee a job at APO, only to have fatal confrontation with Anna/Sydney, while Nadia has her own confrontation with her father over his renewed obsession with Rimbaldi.