Hénaff resumed his underground activities under the pseudonym "Denis", and joined the leadership of the PCF's Organisation Spéciale, where he was responsible for coordinating between the various armed units.
To avoid growing risk of arrest, Hénaff moved in 1943 with his wife and children from Paris to Lyon, where he directed the underground unions in the southern zone and liaised between the FTP and the Main-d'œuvre immigrée (MOI).