On the 10th of March he left Malta for Palermo in the "Foudroyant," sending the ship back, however, to take her place in the blockade, and hoisting his own flag on board a transport. His mind was now rapidly turning towards a final retirement from the station, a decision which was accelerated by the capture of the "Guillaume Tell." This eighty-gun ship started on the night of March 29th to run out from La Valetta, to relieve the famished garrison from feeding the twelve hundred men she carried. Fortunately, the "Foudroyant" had resumed her station off the island; and it was a singular illustration of the good fortune of the "heaven-born" admiral, to repeat Ball's expression, that she arrived barely in time, only a few hours before the event, her absence from which might have resulted in the escape of the enemy, and a just censure upon Nelson. The French ship was sighted first by a frigate, the "Penelope," Captain Blackwood, which hung gallantly upon her quarters, as Nelson in former days had dogged the "Ça Ira" with the "Agamemnon," until the heavier ships could gather round the quarry. The "Guillaume Tell," necessarily intent only on escape from overpowering numbers, could not turn aside to crush the small antagonist, which one of her broadsides might have swept out of existence; yet even so, the frigate decided the issue, for she shot away the main and mizzen topmasts of the French vessel, permitting the remainder of the British to come up. No ship was ever more gallantly fought than the "Guillaume Tell;" the scene would have been well worthy even of Nelson's presence. More could not be said, but Nelson was not there. She had shaken off the "Penelope" and the "Lion," sixty-four, when the "Foudroyant" drew up at six in the morning. "At half-past six," says the latter's log, "shot away the [French] main and mizen-masts: saw a man nail the French ensign to the stump of the mizen-mast. Five minutes past eight, shot away the enemy's foremast. Ten minutes past eight, all her masts being gone by the board, the enemy struck his colours, and ceased firing." The last of the fleet in Aboukir Bay had surrendered to Nelson's ship, but not to Nelson's flag.
"I am sensible," he wrote from Palermo to Sir Edward Berry, the captain of the "Foudroyant," "of your kindness in wishing my presence at the finish of the Egyptian fleet, but I have no cause for sorrow. The thing could not be better done, and I would not for all the world rob you of one particle of your well-earned laurels." In the matter of glory Nelson might well yield much to another, nor miss what he gave; but there is a fitness in things, and it was not fitting that the commander of the division should have been away from his post when such an event was likely to happen. "My task is done, my health is lost, and the orders of the great Earl St. Vincent are completely fulfilled." "I have wrote to Lord Keith," he tells Spencer, "for permission to return to England, when you will see a broken-hearted man. My spirit cannot submit patiently." But by this time, if the forbearance of the First Lord was not exhausted, his patience very nearly was, and a letter had already been sent, which, while couched in terms of delicate consideration, nevertheless betrayed the profound disappointment that had succeeded to admiration for services so eminent, and for a spirit once so indomitable: "To your letter of the 20th of March, all I shall say is, to express my extreme regret that your health should be such as to oblige you to quit your station off Malta, at a time when I should suppose there must be the finest prospect of its reduction. I should be very sorry that you did not accomplish that business in person, as the Guillaume Tell is your due, and that ship ought not to strike to any other. If the enemy should come into the Mediterranean, and whenever they do, it will be suddenly, I should be much concerned to hear that you learnt of their arrival in that sea, either on shore or in a transport at Palermo."
A nearer approach to censure was soon to follow. On the 9th of May, apparently before Nelson's application for leave to return to England had been received, the Admiralty sent orders to Keith, that if his health rendered him incapable of doing his duty, he was to be permitted to return home by sea when opportunity offered, or by land if he preferred. Earl Spencer wrote him at the same time a private letter, in which disapprobation was too thinly masked by carefully chosen words to escape attention: "It is by no means my wish or intention to call you away from service, but having observed that you have been under the necessity of quitting your station off Malta, on account of your health, which I am persuaded you could not have thought of doing without such necessity, it appeared to me much more advisable for you to come home at once, than to be obliged to remain inactive at Palermo, while active service was going on in other parts of the station. I should still much prefer your remaining to complete the reduction of Malta, which I flatter myself cannot be very far distant, and I still look with anxious expectation to the Guillaume Tell striking to your flag. But if, unfortunately, these agreeable events are to be prevented, by your having too much exhausted yourself in the service to be equal to follow them up, I am quite clear, and I believe I am joined in opinion by all your friends here, that you will be more likely to recover your health and strength in England than in an inactive situation at a Foreign Court, however pleasing the respect and gratitude shown to you for your services may be, and no testimonies of respect and gratitude from that Court to you can be, I am convinced, too great for the very essential services you have rendered it. I trust that you will take in good part what I have taken the liberty to write to you as a friend."
Both these letters reached Nelson in June, at Leghorn, on his way home. The underlying censure did not escape him,—"your two letters gave me much pain," he replied,—but he showed no traces of self-condemnation, or of regret for the past. Lord Minto, who was now ambassador at Vienna, wrote thence in March of this year, before the question of going home was decided: "I have letters from Nelson and Lady Hamilton. It does not seem clear whether he will go home. I hope he will not for his own sake, and he will at least, I hope, take Malta first. He does not seem at all conscious of the sort of discredit he has fallen into, or the cause of it, for he still writes, not wisely, about Lady H. and all that. But it is hard to condemn and use ill a hero, as he is in his own element, for being foolish about a woman who has art enough to make fools of many wiser than an admiral." Many years later, immediately after the parting which he did not then know was the last, Minto said of him, "He is in many points a really great man, in others a baby." Nelson himself, conscious of the diligence which he had used in the administration of his wide command and its varied interests, put out of court all other considerations of propriety. "I trust you and all my friends will believe," he told Spencer, "that mine cannot be an inactive life, although it may not carry all the outward parade of much ado about nothing."
Had the Hamiltons remained in Palermo, Nelson would have been forced to a choice between leaving her and the Mediterranean, or yielding a submission to orders which to the last he never gave, when fairly out of signal distance. But the Foreign Office had decided that Sir William should not return after the leave for which he had applied; and in the beginning of March it was known at Palermo that his successor had been appointed. This Nelson also learned, at the latest, when he came back there on the 16th. To one correspondent he wrote, on the 28th, "Most probably my health will force me to retire in April, for I am worn out with fatigue of body and mind," and his application was sent in on the 6th of the latter month, after news of the "Guillaume Tell's" capture. On the 22d Hamilton presented his letters of recall, and on the 24th he and Lady Hamilton, with a party, embarked on board the "Foudroyant" for a trip to Syracuse and Malta, from which they all returned to Palermo on the first of June. Against this renewed departure Troubridge again remonstrated, in words which showed that he and others saw, in Nelson's determination to abandon the field, the results of infatuation rather than of illness.