While Nelson was in England recovering from the loss of his arm, the war against the French entered a new phase. Peace negotiations, which had been going on intermittently throughout 1797, broke down and so Britain was now working to construct a new coalition against France. At the same time, Admiral Adam Duncan's victory over the Dutch at Camperdown on 11 October finally ended the threat of invasion, which had been hanging over Britain for more than a year, and so the Cabinet now felt able to look once again at the situation in the Mediterranean. Britain's withdrawal of her fleet in 1796 had been used by the Austrians to justify their own withdrawal from the war, and ministers knew that if they wished to construct a new coalition they had to make a show of strength in the sea again. Moreover, they were beginning to receive intelligence reports of a major expeditionary force being prepared at Toulon. So the idea began to grow of sending a special detached squadron to operate there independently. It would be a highly responsible command for which special qualities of leadership would be needed – and, suddenly, everybody seemed to think of Nelson. Having hoisted his flag in the 74-gun battleship, HMS Vanguard, he rejoined the fleet off Cadiz in May and was detached again almost at once on a special mission into the Mediterranean.

The French were planning a bold and imaginative stroke that they hoped might win the war for them: an invasion of Egypt, followed by an overland attack on British trade in India. In overall command was the brilliant young General Napoleon Bonaparte, fresh from his recent conquest of Italy. Sailing on 19 May 1798 with 35,000 troops in 400 transports, escorted by thirteen battleships, the French went first to Malta, which was surrendered without a fight, and from there to Egypt, where they arrived on 1 July. The army was landed without opposition and, by the end of the month, Egypt was under French control.