The present disclosure relates to an electromechanical surgical system (10) and methods for use thereof including a surgical instrument (100) having a controller (150), and an end effector (300) selectively and removably connectable to the surgical instrument, wherein the controller enters an emergency retraction mode (540, 640, 740) when at least one input element (124, 126, 128, 130) of the surgical system is incapable of providing control signals to the controller to operate a motor (166), wherein the emergency retraction mode activates the motor to withdraw a drive assembly (360) from any advanced position thereof.