Brace's period of command was brief, he was superseded by Captain Francis Austen on 12 September. With the draw down in hostilities prior to the signing of the Treaty of Amiens in March 1802, Neptune was one of the many ships of the Mediterranean fleet to be ordered home, arriving at Portsmouth on 24 February. Austen paid her off on 29 April, but recommissioned her the next day. Neptune then underwent a brief refit, during which £5,728 was expended, £2,895 of which was spent on her hull, masts and yards. Austen was superseded on 30 September 1802 and the following day Captain William O'Bryen Drury took command. With Neptune fully refitted and stored, she sailed from the dockyard and joined the Channel Fleet at Spithead on 29 October. Blockade, and approach to Trafalgar Drury commanded Neptune for the next two years, until his promotion to rear-admiral in 1804. He departed the ship on 13 May 1804, and the following day Captain Sir Thomas Williams took over. Neptune spent the rest of 1804 deployed with the Channel Fleet, blockading the French Atlantic ports. During this time Captain Williams' health progressively worsened, and he was invalided back to Britain on 7 May 1805. He was replaced by Captain Thomas Fremantle on 8 May, and was sent to join Robert Calder's force blockading Ferrol, after the Franco-Spanish fleet had arrived there after the Battle of Cape Finisterre. Calder decided that his eight ships were not sufficient to resist Villeneuve's fleet were it to come out of harbour, and instead went north to join Admiral William Cornwallis's fleet off Brest. Shortly afterwards Nelson's fleet returned from the West Indies, bringing 12 more ships, and Calder was given 18 ships, including Neptune, and sent back to Ferrol to search for Villeneuve. By now Villeneuve had put into Cadiz and Calder's force was ordered to join the hastily assembled British fleet under Vice-Admiral Cuthbert Collingwood, that was blockading the Franco-Spanish fleet at Cadiz. As the British fleet settled in for a long blockade Fremantle commented on Neptunes sailing qualities. She had the reputation of being slow, and Fremantle complained that he did not like being in 'a large ship that don't sail and must continually be late in action.' During the battle however, Midshipman William Baddock commented that 'The old Neptune, which never was a good sailer, took it into her head that morning to sail