The defection of the Monsieur was, however, only the beginning of Jones's troubles with the insubordinate officers. While attempting to capture a brigantine, Jones, through the desertion of some of his English sailors, lost two of his small boats, for which he was bitterly and unjustly reproached by the crazy, incompetent, and greedy Landais, captain of the Alliance, who said that hereafter he would chase in the manner he saw fit. Shortly afterwards, the Cerf abruptly left the fleet, and the other privateer also went off on its own account. Jones was left with only the Bonhomme Richard, the Pallas, the Vengeance, and the Alliance; and it would have been better, as the result showed, if the last-mentioned vessel and its extraordinary captain had also decamped at this time for good. Landais paid no attention to Jones's signals, but left the squadron for days, unfortunately returning. Against Jones's orders he sent two prizes into Bergen, Norway, where they were given by the Danish government to the English, and were for many years after the war a source of trouble between Denmark and the United States.
Jones was also compelled to treat with the other French captains, and several times modified his course in compliance with their demands. He had formed a daring design to lay Leith, on the coast of Scotland, and perhaps Edinburgh, under contribution, but first he had to argue the matter with his captains. Fanning says: "Jones displayed so artfully his arguments in favor of his plan that it was agreed pretty unanimously to put it in immediate execution." Jones's art was manifested in this instance, according to his account, by showing the captains "a large heap of gold at the end of the prospect." During this enforced conference, however, the wind shifted, and the undertaking had to be given up. Fanning quaintly remarks: "All his [Jones's] vast projects of wealth and aggrandizement became at once a shadow that passeth away, never more to appear again!"
Jones, however, said that he would have succeeded, even at this late hour, if his plan had been followed, and showed a touch of the weak side of his character when he added: "Nothing prevented me from pursuing my design but the reproach that would have been cast upon my character, as a man of prudence, had the enterprise miscarried. It would have been said: 'Was he not forewarned by Captain Cottineau and others?'"
With his old ship, his motley squadron, and his insubordinate officers, Jones then cruised along the Yorkshire coast, destroyed or captured a number of vessels, and was preparing to end his voyage at the Texel, Holland, when chance threw in his way the opportunity which he so greatly embraced.
On the 23d of September the squadron was chasing a ship off Flamborough Head, when the Baltic fleet of merchantmen, for which Jones had been looking, hove in sight. The commodore hoisted the signal for a general chase. Landais, however, ignored the signal and went off by himself. The merchant ships, when they saw Jones's squadron bearing down upon them, made for the shore and escaped, protected by two ships of war, frigates, which stood out and made preparations to fight, in order to save their convoy.
These British ships of war were the Serapis, a new frigate of forty-four guns, and the Countess of Scarborough, twenty guns. The Alliance, at that time, which was late in the afternoon, was not in sight, and the little Vengeance, which had been sent to look for Landais, was also not available. There were, therefore, two ships on each side, and Jones ordered Captain Cottineau, of the Pallas, to look after the Countess of Scarborough, while he himself took care of the Serapis. Jones never lost his head in action, and yet he decided, with that "cool, determined bravery," of which Benjamin Franklin spoke, and with "that presence of mind which never deserted him" in action, recorded by Fanning, to engage a ship known by him to be the superior of the Bonhomme Richard in almost every respect. It has been said of Jones by one who fought with him that only in battle was he absolutely at ease: only at times of comparative inaction, when he could not exert himself fully, was he restless and irritable. On this occasion he joyfully engaged a ship which threw a weight of metal superior to his by three to two, that sailed much faster, and was consequently at an advantage in manœuvring for position, and that had a crew equal to that of Jones in numbers, and far more disciplined and homogeneous. A battle resulted which for desperate fighting has never been excelled, and perhaps never equaled on the sea.