The peace proved short-lived, however, for at the end of 1798 a new coalition directed against France was formed (the War of the Second Coalition, 1798–1802). This time Prussia remained neutral. Frederick William III, a conscientious and modest but ineffectual ruler, was notable for private morality rather than political skill. The government in Berlin drifted back and forth, dabbling in minor economic and administrative reforms without significantly improving the structure of the state. A decade of neutrality was frittered away while the army commanders rested on the laurels of Frederick the Great. Austria, on the other hand, played the same leading role in the War of the Second Coalition that it did in the War of the First Coalition, with the same unfortunate result. The French victories at Marengo (June 14, 1800) and Hohenlinden (December 3, 1800) forced Emperor Francis II to agree to the Treaty of Lunéville (February 9, 1801), which confirmed the cession of the Rhineland. More than that, those rulers who lost their possessions on the left bank under the terms of the peace were to receive compensation elsewhere in the empire. In order to carry out this redistribution of territory, the Imperial Diet entrusted a committee of princes, the Reichsdeputation, with the task of drawing a new map of Germany. France, however, exercised the major influence over its deliberations. Napoleon had resolved to utilize the settlement of territorial claims to fundamentally alter the structure of the Holy Roman Empire. The result was that the Final Recess (Hauptschluss) of the Reichsdeputation of February 1803 marked the end of the old order in Germany. In their attempt to establish a chain of satellite states east of the Rhine, the French diplomats brought about the elimination of the smallest and least viable of the political components of Germany. They thereby also furthered the process of national consolidation, since the fragmentation of civic authority in the empire had been a mainstay of particularism. That Napoleon did not intend to encourage unity among his neighbors goes without saying. Yet he unwittingly prepared the way for a process of centralization in Germany that helped to frustrate his own plans for the future aggrandizement of France.

The chief victims of the Final Recess were the free cities, the imperial knights, and the ecclesiastical territories. They fell by the dozens. Too weak to be useful allies of Napoleon, they were destroyed by the ambition of their French conquerors and by the greed of their German neighbors. They could still boast of their ancient history as sovereign members of the Holy Roman Empire, but their continued existence had become incompatible with effective government in Germany. The principal heirs to their holdings were the larger secondary states. To be sure, Napoleon could not keep Austria and Prussia from making some gains in the general scramble for territory that they had helped make possible. But he worked to aggrandize those German rulers, most of them in the south, who were strong enough to be valuable vassals but not strong enough to be potential threats. Bavaria, Württemberg, Baden, Hesse-Darmstadt, and Nassau were the big winners in the competition for booty that had been the main object of the negotiations. Napoleon’s strategy had been in the classic tradition of French diplomacy, the tradition of Richelieu and Mazarin. The princes had been pitted against the emperor to enhance the role that Paris could play in the affairs of the German states. Yet the German princes did not resent being used as pawns in a political game to promote the interests of a foreign power. Whatever objections they raised against the settlement of 1803 were based on expediency and opportunism. The most serious indictment of the old order was that in the hour of its imminent collapse none of the rulers attempted to defend it in the name of the general welfare of Germany.

The Final Recess was the next to last act in the fall of the Holy Roman Empire. The end came three years later. In 1805 Austria joined the third coalition of Great Powers determined to reduce the preponderance of France (resulting in the War of the Third Coalition, 1805–07). The outcome of this war was even more disastrous than those of the wars of the first and second coalitions. Napoleon forced the main Habsburg army in Germany to surrender at Ulm (October 17, 1805); then he descended on Vienna, occupying the proud capital of his enemy; and finally he inflicted a crushing defeat (December 2, 1805) on the combined Russian and Austrian armies at Austerlitz in Moravia (now in the Czech Republic). Before the year was out, Francis II was forced to sign the humiliating Treaty of Pressburg (December 26), which ended the dominant role his dynasty had played in the affairs of Germany. He had to surrender his possessions in western Germany to Württemberg and Baden, and the province of Tirol to Bavaria. Napoleon’s strategy of playing princely against imperial ambitions had proved a brilliant success. The rulers of the secondary states in the south had supported him in the war against Austria, and in the peace that ensued they were richly rewarded. Not only did they share in the booty seized from the Habsburgs, but they also were permitted to absorb the remaining free cities, petty principalities, and ecclesiastical territories. Finally, asserting the rights of full sovereignty, the rulers of Bavaria and Württemberg assumed the title of king, while the rulers of Baden and Hesse-Darmstadt contented themselves with the more modest rank of grand duke. The last vestiges of the imperial constitution had now been destroyed, and Germany was ready for a new form of political organization reflecting power relationships created by the force of arms.

In the summer of 1806, 16 of the secondary states, encouraged and prodded by Paris, announced that they were forming a separate association to be known as the Confederation of the Rhine. Archbishop Karl Theodor von Dalberg was to preside over the new union as the “prince primate,” while future deliberations among the members were to establish a college of kings and a college of princes as common legislative bodies. There was even talk of a “fundamental statute” that would serve as the constitution of a rejuvenated Germany. Yet all these brave plans were never more than a facade for the harsh reality of alien hegemony in Germany. Napoleon was proclaimed the “protector” of the Confederation of the Rhine, and a permanent alliance between the member states and the French Empire obliged the former to maintain substantial military forces for the purpose of mutual defense. There could be no doubt whose interests these troops would serve. The secondary rulers of Germany were expected to pay a handsome tribute to Paris for their newly acquired sham sovereignty. On August 1 the confederated states proclaimed their secession from the empire, and a week later, on August 6, 1806, Francis II announced that he was laying down the imperial crown. The Holy Roman Empire thus came officially to an end after a history of a thousand years.