Thomas eventually returned to England and in December 1803 was appointed to command of the bomb vessel , to serve in the Mediterranean. On 22 October 1805, following the victory at Trafalgar, he was posted into briefly, before serving aboard the , and as flag captain to Lord Collingwood, engaged primarily on the blockade of Toulon. His position was a particularly arduous one, there being no Captain of the Fleet, and Collingwood was for much of the time severely ill with the cancer that would eventually kill him in March 1810. After Collingwood's death Thomas served as captain of the Ville de Paris until December 1810. The following February he was appointed to command of the frigate initially engaged on operations on the coast of Catalonia, then on the blockade of Marseilles and Toulon. He was eventually invalided home in February 1813, and saw no further wartime service.
