In the year following his double appointment as minister for the war and marine, Clarke made the German campaign on the staff of Bonaparte, and was present at the capture of the free city of Ulm, in the Swabian circle, on the 17th October, 1805, and at other operations, which drove the army of the Archduke Ferdinand across the Danube; and, on the capture of Vienna by the corps of the brave Murat and Lannes, he was named governor of the city and also of Upper and Lower Austria, Carinthia, Styria, Friuli, Trieste, &c. His moderation and justice in this high command elevated him among the victors, and won him the love and esteem of the vanquished. He also received the cordon of Grand Officer of the Legion of Honour, and soon after was ordered to define the line of demarcation between Brisgau, in the kingdom of Wirtemberg, and the Grand Duchy of Baden.
Two months were spent by him in conferences and diplomacy. From the 9th to the 20th of July, 1806, he was engaged with the Russian plenipotentiary, and their interviews were terminated by the wonderful treaty which opened and ceded to France, Cattaro, a Venetian territory in Dalmatia, with its capital, harbour, and citadel; and which maintained Gustavus IV. in possession of the ancient Duchy of Pomerania, and left to be achieved, at an early period, the junction of Sicily to the kingdom of Murat--the whole being arranged by them, without condescending to ask the advice of Great Britain, which was then the faithful ally of Prussia. This treaty was never ratified by the Emperor Alexander. The other conferences took place between Clarke and Lord Yarmouth, to whom Charles Fox added the Scottish Earl of Lauderdale; while, to assist Clarke, the French government added Jean Baptiste Champagny, the Duc de Cadore, who was only a spectator of the negotiations, which were without result, and are of no consequence to the reader; but Clarke, who had displayed his usual acuteness, tact, and skill in all his meetings with the Lords Yarmouth and Lauderdale, was not a little proud of having prevailed upon M. D'Oubril to sign certain clauses he submitted to him.
Russia, however, was in no haste to evacuate Cattaro, and the Emperor Alexander began to augment his army; so from September, 1806, it became evident that if France declared war against Prussia, she would have to encounter Russia also. In the first meeting concerning these affairs Clarke said, "that the convention recently concluded with Russia was for France equivalent to a victory; and that henceforward his master, the Emperor Napoleon, had the right of proposing articles more advantageous than those he had lately made." He qualified the terms of the treaty which he wished them to adopt, and in particular _l'uti possedetis_; of vague conversations on the politics of Rome, he said that Bonaparte had never adopted this _uti possedetis_ for a basis, without which Moravia, Styria, and Carniola would have remained still in his hands.