Sydney is sent to Madrid to retrieve a 500-year-old sketch that contains a set of numbers and meets up with her deadly nemesis, K-Directorate agent, Anna Espinosa. Meanwhile, Will digs deeper into the cause of Danny's death and finds some odd information.

Sydney must undergo an extensive lie detector test to prove her loyalty to SD-6 while at the same time she is trying to find connection between a 500 year old Rambaldi sketch and a machine. In the meantime, Will gets deeper into the secrets while investigating Danny's death.

After the SD-6 finds out that another terrorist organisation was attacked at the same time as them, Sydney and Dixon are sent to Las Vegas, and later Moscow, to try to find something that will bring SD-6 closer to identity of The Man. All in the same time, Sydney learns some shocking news about Francie's fiancé, Jack tries to be a better father to Sydney and Will begins his journey in discovering SD-6.

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.