Beaver had hoped for a promotion after the victory, but this turn of events meant that it was not to be and he returned to Keith. He was detained at Gibraltar for a fortnight whilst making his return, and so took the opportunity to marry his young fiancée, Miss Elliott. He went on to rejoin Lord Keith, and was promoted to captain on 10 January 1801. He received the prestigious appointment to command the flagship, and took an active role in the operations on the coast of Egypt from 1800 to 1801. He quickly tired of the monotony of maintaining a blockade and obtained permission to take the frigate HMS "Déterminée" to Constantinople with dispatches. The Sultan wanted to acknowledge Beaver's services, and offered him a large sum of money, which Beaver refused. He did however accept a diamond box for himself and a gold box for each of the lieutenants. Beaver was also rewarded with the Order of the Crescent. The Peace of Amiens temporarily ended the war with France, and Beaver and the "Déterminée" were ordered home. The "Déterminée" was paid off at Portsmouth on 19 May 1802, and Beaver was put in charge of the sea fencibles of Essex in July 1803. He was highly successful in these duties, and three years later returned to sea, having been appointed to command the 40-gun frigate HMS "Acasta". He sailed her to the West Indies, remaining there until after the capture of Martinique in February 1809. He returned to England and after a few months, was appointed to command the 38-gun HMS "Nisus", departing aboard her for the East Indies on 22 June 1810. He arrived on the station and joined the squadron under the command of Vice-Admiral Sir Albemarle Bertie. Beaver played a distinguished part in the capture of Mauritius in November 1810. Beaver and the "Nisus" then moved to a squadron under Rear-Admiral Robert Stopford and took part in the conquest of Java in August and September 1811. He spent nearly a year in Mozambique and off the coast of Madagascar, and received orders by the end of 1812 to return to England. The "Nisus" was making her return voyage, when she put into Table Bay towards the end of March 1813. Beaver had complained of a slight indisposition previously, but became seized by a violent inflammation of the bowels. He spent a few days in excruciating pain, before dying on 5 April 1813.