Willot transferred to the War in the Vendée where he served until spring 1796. During this period he was temporarily in command of the "Army of the West". He was in charge of the 8th Military Division at Marseilles until his election to the Council of Five Hundred in April 1797. He aligned himself with the Royalists who were regarded as a threat by powerful men in the French Directory. After the Coup of 18 Fructidor he was deported to French Guiana with others belonging to Pichegru's faction, but later escaped. Willot overtly embraced the Royalist cause and worked with France's enemies to overthrow the First French Republic. After drifting to several nations, he spent the years of the First French Empire in the United States. Returning to France with King Louis XVIII he was ennobled as a count and given awards for his loyalty. His surname is one of the names inscribed under the Arc de Triomphe, on Column 34.