Following the theft of a deadly virus, code named Substance 33, in Turkey, Sydney is forced to partner on a mission with new APO agent Thomas Grace where they and Marshall travel to Prauge to look for the stolen virus container where their paths cross with Rachel Gibson, a spy suspected of being involved in activities against the U.S., has something shockingly in common with Sydney that she's working for a black ops group called The Shed, that is run by Gordon Dean and his murderous associate Kelly Peyton. Sydney and Tom must persuade Rachel to infiltrate The Shed to download Dean's computer files to learn where Substance 33 is being hidden. Meanwhile, Dixon must accompany Sloane, who's given a 48-hour pass from prison to acquire a possible cure for his still-comatose daughter, Nadia, from a scientist in Russia.