Truget called upon Missiessy again in October 1801, when he needed someone to command a squadron of ships at Brest. Missiessy held the post until  10 September 1804, when he was appointed commander-in-chief of the Rochefort squadron. The Rochefort squadron was a key element in Napoleon's planned invasion of the United Kingdom; intended to rendezvous with Villeneuve's fleet in the West Indies and draw British ships there, before racing back across the Atlantic and seizing control of the English Channel. On 11 January 1805 the blockading British ships were blown off station, allowing Missiessy's force to escape. Aboard the five ships-of-the-line, three frigates and two corvettes were 3500 troops under General Joseph Lagrange and artillery, supplies and weapons to reinforce the French garrisons of Martinique, Guadeloupe and Saint-Domingue. The same wind that disrupted the British blockade, kept the French ships pinned to the coast for five days, delaying arrival in Martinique until 20 February.