Ignoring her request to call off the sniper who’s protecting her, Red alerts Liz to the re-emergence of Maddox and Carrie Ann Beck, ecoterrorists who were thought dead until Carrie Ann turned up in a hospital on life support after being hit by a taxi during a scuffle with her husband. As Red suspects Beck left his wife to die for opposing his radical views, Aram identifies the red clay under Carrie’s fingernails as being from a 14th-century painting that the Becks recently stole from a Spanish museum. After Aram then discovers a concealed map hidden in the painting, art historian Lillian Sharpe links it to the legend of the Apophis Strain, thought to be the origin of the Black Death and which was hidden hundreds of years ago.
Though Lillian tells Cooper the map is worthless, she tells Red and Liz that it places the corpse of an infected priest in a Staten Island cemetery. But after Aram learns that the body was moved years ago to Manhattan’s Holy Trinity Church, Liz and Ressler are unable to keep Beck from escaping with bones containing DNA from the ancient virus. Meanwhile, after tracker Glen Carter comes up empty-handed, Red enlists Aram to look for his daughter. But when Liz learns of their arrangement, she insists that Red stop using Aram while she works to put the sniper off her trail.
In a twisted plan to save the world, Beck starts infecting his followers with the plague and sending them out to kill off humankind, beginning with the citizens of Washington, D.C. Using a clue uncovered by Aram, Liz and Samar stop an infected Chris Perez from boarding a plane for Toronto. In the ensuing struggle, Perez infects Samar before Liz can shoot him. Despite the danger of becoming ill, Liz stays with Samar at the airport as the CDC looks to develop a cure before it’s too late. Uncovering the ecoterrorist’s location, Red lures Beck into a trap and, after forcing Beck’s girlfriend Pepper to give him a mysterious old key she’s been hiding, walks away with the antidote they made to save themselves. Finally, after giving the antidote to the FBI to stop the plague and save Liz and Samar, Red learns that Glen has found his daughter.