From the beginning of the invasion, there was an English squadron blocking the mouth of the Tagus, commanded by Admiral Sir Charles Cotton (Fig. 10), 5th Baron of Landwade.
Of course, it was Admiral Sir Sidney Smith who was in command, blockading the Tagus, at the beginning of the invasion. Cook came along to take over, some time later; Smith having returned to blockade Lisbon only because of the presence of the Russian fleet in that harbor.
Since spring he (Cook) had been issuing proclamations, exhorting the Portuguese to revolt against the invader. Adherence to the rebellion and especially the arrest of the French governor could lead to vicious revenge. Thus it is no wonder that the first measure taken by the councils of Santiago do Cacém and Sines was to seek help from the admiral. As early as the 28th, each of the two villages, in turn, sent letters to Sir Charles.
Admiral Cotton responded early on July 1 by sending the Comus frigate commanded by Captain Matthew Smith to Sines, where he arrived on the 2nd with weapons, gunpowder and ammunition to distribute for the rebels. Comus remained at Sines, with some trips to the fleet, at the mouth of the Tagus, carrying prisoners there and arms and ammunition here until nearly the end of the invasion.
This is interesting information about the Cook supplying arms to the rebels, via the Comus or otherwise, which, to my recall, is not available in any account in English. Maybe it is in "In the Shadow of Nelson: The Naval Leadership of Admiral Sir Charles Cotton, 1753-1812 " but I don't recollect it.