Sgts. Michael Stonebridge and Damien Scott are shocked to discover that Leo Kamali is not only alive, but he's been running the terrorist operation since al-Zuhari was killed in a drone strike six months earlier. Kamali's guards intend to deliver the boys to Arkady Ulyanov, but they escape and take their driver hostage. They torture the man and learn the terrorists' plan: to expose American and British soldiers at Ramstein airbase to the smallpox virus.
Richmond discovers the identities of the "clean skins," fake profiles Andersson installed in NATO's system. The airbase goes on lockdown as photos of the terrorists disguised as maintenance crew, medical and flight staff, and Military Police are circulated. Martinez, recovering from a gunshot wound in the hospital ward, recognizes a clean skin posing as a doctor. The terrorist is subdued, but not before she sprays smallpox into the room. Martinez and the other patients are quarantined.
The boys take down three of the undercover terrorists and discover their plan to disperse the virus through the filters in the building's ventilation system. They're able to protect the basement system, but Kamali escapes and boards a plane with the virus. He and Qassem devise a new plan: release the virus over the city by air. Stonebridge, Scott and Richmond board the plane in pursuit, but the Air Force has ordered that it be shot down. They escape just before the missile hits, as does Leo Kamali.
Ulyanov follows through on a deal he made with Locke; he gives up Kamali in exchange for his son's killers - Scott and Stonebridge. Locke informs the boys he's traded them for the virus' cure. Fearing the worst, Scott finally reaches out to his son. Ulyanov forces Kamali into a public square by threatening Ester's life. Kamali reveals he's pocketed the virus and threatens to release it into the crowd. The boys are forced to shoot him, and Nina takes advantage of the chaos to kill Ulyanov. At Ester's begging, Kamali uses his last breath to reveal the virus' cure is in Ester's locket. The infected patients from the airbase are saved and Section 20 celebrates a mission accomplished.