Nelson immediately asked to be relieved. “I do feel, for I am a man,” he wrote to St. Vincent, “that it is impossible for me to serve in these seas, with the squadron under a junior officer.  Never, never was I so astonished.”  With this private letter he sent an official application for leave.  “The great anxiety I have undergone during the whole time I have been honoured with this important command, has much impaired a weak constitution.  And now, finding that much abler officers are arrived within the district which I had thought under my command, ... and, I flatter myself, having made the British nation and our gracious Sovereign more beloved and respected than heretofore; under these circumstances I entreat, that if my health and uneasiness of mind should not be mended, that I may have your Lordship’s permission to leave this command to my gallant and most excellent second in command, Captain Troubridge.”  In similar terms, though more guarded, he wrote to Earl Spencer.  At the same time he took proper steps to prevent the official impropriety, not to say rudeness, which Smith was about to commit by taking from Hood his charge, without either the latter or Nelson receiving personal instructions to surrender it.  He sent Troubridge hastily to Alexandria to take command there, with orders that, upon Smith’s arrival, he should deliver up the blockade to him, and return to the westward.  “I should hope,” he wrote to Spencer, “that Sir Sidney Smith will not take any ship from under my command, without my orders;” but he evidently expected that he would, and was determined to forestall the possibility of such an affront.

Nelson’s services had been so eminent, and were at this time so indispensable, and his exceptions to the manner in which Smith had been intruded into his command were so well founded, that the matter was rectified as rapidly as the slow round of communications in that day would permit.  The Admiralty disclaimed any intention of circumscribing his control in the Mediterranean, and Smith received peremptory orders from St. Vincent to report himself to Nelson by letter for orders.  The latter of course carried out the Admiralty’s wishes, by intrusting to Smith the immediate direction of operations in the Levant, while retaining in his own hands the general outlines of naval policy.  He kept a very tight rein on Smith, however, and introduced into the situation some dry humor, unusual with him.  The two brothers, envoys, he addressed jointly, in his official letters, by the collective term “Your Excellency.”  “I beg of your Excellency,” he says in such a letter, “to forward my letter to Sir Sidney Smith, Captain of the Tigre.  I have this day received letters from Sir Sidney Smith, in his Ministerial capacity, I believe.  I wish that all Ministerial letters should be written in your joint names; for it may be difficult for me to distinguish the Captain of the man-of-war from the Joint Minister, and the propriety of language in one might be very proper to what it is in the other.”  To the naval captain he writes:  “I must direct you, whenever you have Ministerial affairs to communicate, that it is done jointly with your respectable brother, and not mix naval business with the other.  I have sent you my orders, which your abilities as a sea-officer will lead you to punctually execute.”