In the season premiere, Nostradamus attends the gathering concerning the Plague. He describes the symptoms of the plague to everyone at court. He then volunteers to go look for Francis and Lola in the village on behalf of Catherine and Mary, believing that he is immune to the plague. When he returns, he tells the two that the house Francis and Lola stayed in a house that had been marked with a red x, signifying the plague and that the villagers had burned the house down soon after. Later, he and Mary give Catherine something to make her think she'd come down with the plague so she wouldn't command the murder of the Valents. He also helps Mary in killing Éduard Narcisse, locking him in a room with those effected with the plague.
In Drawn and Quartered, Nostradamus faces the consequences of helping Mary kill Éduard. When Éduard's father, Stéphane Narcisse, finds out that his son was "misdiagnosed" by Nostradamus and put in an infected room to die. Regardless of the fact that Narcisse learnt the truth about his son's death, he and the other nobles demand that Nostradamus be drawn and quartered. When Nostradamus is about to be drawn and quartered, Mary stops it and saves his life with the help of a plan she made with Francis. Not long after, Nostradamus leaves court on horseback.
Nostradamus returns in Burn. He is seen talking to Francis whom has still not recovered and is dying.