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The German Habsburgs were forced to take the defensive and their cause was in great danger. Allied with Maximilian they were compelled to use their main force to prevent the occupation of southern Germany by the French. They bravely fought in this part of Germany under Mercy during the years 1643-45, but were continually obliged to fall back. On 5 May, 1645, they gained a famous victory over Turenne at Mergentheim; on 3 August, 1645, the French were victorious at Allersheim and Mercy was killed. Still the imperial and Bavarian troops were always at least strong enough to save Bavaria from the incursions of the French. In the meantime, however, the imperial forces had not been able to bring a sufficiently large army against the Swedes. These, it is true, were obliged to encounter (1642) a new enemy in Denmark. But the Danes accomplished just as little as their imperial allies. The imperial forces were severely defeated by Torstenson at Breitenfeld in November, 1642, and at Jüterbogk and Magdeburg in October, 1644. After these two victories, Torstenson formed an alliance with George Rákóczy, the successor to Bethlen Gabor as Prince of Transylvania. Resolved to carry the war directly into the hereditary lands of the emperor, Torstenson advanced at once as far as Brünn, but there saw that he was too weak for such an undertaking. The result of the Swedish victories in this year was the permanent loss by the imperialists of the control of the Weser, and of their position in northwestern Germany. Denmark concluded a treaty of peace in 1645.
During the years 1642-45 the German estates unceasingly demanded peace. As early as 1640, at a session of the Electors at Nuremberg, the opinion was expressed, that a part of Pomerania should be ceded to the Swedes if this would content them. In 1641 at the suggestion of the electors the first Diet held since 1613 met at Ratisbon, and its success proved that the effort made in the Peace of Prague to revive the organization of the empire had borne good fruit. The Diet granted the emperor considerable subsidies. The estates, however, showed very plainly that they believed the emperor was over-considerate of Spain. France and Sweden encouraged this view by expressing their readiness to open negotiations. The opinion gained ground among the estates that if Austria did not break off its connexion with Spain the estates would once more abandon the emperor, form a union among themselves, and make a treaty of peace for the empire with France and Sweden. The estates hoped that these two countries would consent not to interfere in the internal affairs of the empire, especially as regards religion. The economic suffering and misery of the population of the empire had greatly increased, largely through the marauding expeditions of the Swedes, and final success in the war was clearly out of the question. John Philip von Schönborn, Bishop of Würzburg, was especially active in supporting the proposal that the estates should separate from the emperor and establish peace in the empire without him. Maximilian encouraged the bishop, though reluctantly. One after another, the smaller German estates brought letters of protection from the Swedes in order to escape being plundered by them. In this way these territories became neutral without any further formalities. Of the larger principalities Brandenburg abandoned its neutrality in 1644 without, however, becoming friendly to the emperor on this account. On the other hand, Saxony, which was exhausted and desperate, made a direct treaty of neutrality with Sweden in 1645. Under these circumstances the emperor early in 1643 also declared himself ready to negotiate. He wished, however, that the treaty of peace should be general, not limited in geographical extent as was the case in 1630. The negotiations were to be carried on with France at Münster, with Sweden at Osnabrück, where the Swedish embassy had been since the spring of 1643. About the middle of 1643 the imperial delegates appeared at both designated places, and the French delegates followed in the spring of 1644. At the close of 1644, the imperial delegates presented their first proposition, to which the French did not reply until November, 1645. A last dispute had arisen over the question whether the emperor alone should negotiate for the empire or whether the estates should also be represented. The quarrel was practically settled by the invitation to be present sent to the various estates by France and Sweden. On 26 August, 1645, the emperor also invited them. In the same year representatives of Spain and Holland also appeared at Münster. An ambassador of Venice and a papal nuncio likewise took part as mediators between France and the emperor.
The course of the negotiations was influenced by the results of the last events of the war, and it was decided by the military conditions of 1646. In this year the Swedes under Wrangel united with Turenne and the two armies occupied Bavaria. This led Maximilian to make a treaty of neutrality with Sweden in March, 1647. The entire empire was now occupied by the armies of France and Sweden, but the emperor retained undisputed possession of his hereditary lands. The outbreaks of the years 1647-48 were directed against him. The French, however, could not aid these revolts, as internal troubles in France claimed their attention and made them desirous of coming to a settlement with the emperor and the empire. While Turenne marched back to France (1647) Wrangel seized Prague, but was expelled by the emperor and Maximilian, who broke his agreement with Sweden. In 1648 Turenne appeared again and, allied with the Swedes, defeated the imperial and Bavarian forces at Zusmarhausen and cruelly ravaged Bavaria. The attack on Prague was renewed by the Swedes alone in July, 1648, under Königsmark. They took part of the city, but the Austrians brought together a larger army and forced them to withdraw in November, 1648.

At the opening of the negotiations for peace the emperor had hoped to be able to indemnify Sweden and to separate it from France, but on Sweden's refusal to accept his proposals he was obliged to give up his intention of making peace only if Spain were included in it. Supported by Maximilian, France induced the emperor and empire to remain neutral during the Franco-Spanish war. This success for France, however, did not prevent Holland from concluding peace with Spain on 5 June, 1648. But France received recompense for this disappointment in a new and great victory of Condé at Lens in the Netherlands, on 20 August, 1648. To secure peace for the empire, Austria consented in 1648 to give up its hereditary lands in Alsace and the city of Breisach to France; it also finally recognized the incorporation of the territories of Metz, Toul, and Verdun into France. It postponed, however, the decision as to the claims of France on the Duchy of Lorraine, and prevented France being made an estate of the empire for its conquests in Alsace. Sweden received the land around the mouth of the Oder with Stettin and Hither Pomerania, the territory near the outlet of the Weser, and the dioceses of Bremen and Verden, as well as Wismar, and was made an estate of the empire, because it and not the Electorate of Saxony, had been the leader of the Protestant estates in the negotiations for peace. In addition it was to receive money to pay its mercenaries.
Taken in general, all the states and territories of the empire were confirmed in the possessions that they had had in 1618. The exceptions were: Electoral Saxony was confirmed in the possession of Lusatia which had been conceded to it in 1620; Bavaria was left in possession of the Upper Palatinate and of the fourth electorship, while a new, eighth electorate was created for the Palatinate; by the intervention of France, Brandenburg received, besides Further Pomerania, a number of dioceses with the right to secularize them. This and the similar concession to Sweden for Bremen and Verden undermined one of the main foundations of the organization of the empire, which for hundreds of years had rested on the existence and importance of the spiritual domains. In other particulars it was evident that the more important states sought, and probably sincerely, not to damage the efforts made in the Peace of Prague to revive the organization of the empire, yet in various instances they inflicted much injury upon it. It was contrary to the organization of the empire that the negotiations, deviating from the original intention, were not limited to external matters. Sweden and a large number of the Protestant estates were not willing to consent to this. To settle the claims made by the different religious denominations to one and the same territory the year 1624 was taken as the normal year, and the denomination which had prevailed in that year in a territory, was, as a rule, to be the permanent religion of that territory. Calvinism was included in the religious peace. The compulsory force of the principle, cujus regio, ejus religio, was restricted by granting private liberty of conscience, but only to a limited extent. The result of these regulations was in the main that the period of the violent religious disputes which had divided the empire was closed. It was also hoped that an effective working of the organic parts of the empire -- the imperial and provincial diets, the supreme court, the Aulic Council, and the district constitution -- would be secured for the future by an arrangement of their relations with one another and of their authority. The details of this reconstruction were left to the decision of a future Diet. It was settled, however, that grants of supplies were to be made not by majority votes, but by the voluntary agreement of the estates. All the rulers, even the petty ones in southern and western Germany, were declared sovereign in the internal government of their territories with certain exceptions. Moreover, the right to have diplomatic relations with foreign countries and to make treaties with them was granted to every estate. In reality this regulation only gave legal recognition to conditions that actually existed.
Austria was exempt from all these regulations, especially from the changes in the canon law prevailing there. This showed how little injury the war had inflicted upon it, and also the increasing differentiation between its domains and those of the other estates of the empire. The seal was impressed upon this differentiation by the fact that France secured (1647) the appointment of John Philip von Schönborn as Elector of Mainz and consequently Chancellor of the Empire, and especially by the fact that the treaty conceded to France and Sweden lasting diplomatic influence in the empire in return for their evacuation of the imperial territories. To counterbalance the influence which Austria exercised within the empire in virtue of her possession of the imperial crown, France and Sweden received the right to superintend the execution of the treaty in the empire, consequently to continually interfere in imperial affairs. On this basis the Peace of Westphalia with France and Sweden was settled on 24 October, 1648. The chief results of the Thirty Years War were: the foundation and recognition of a unified Austria under the rule of the German Habsburgs; the revival, in a certain doubtful sense though of the Holy Roman Empire; the establishment of Sweden on German soil; the permanent weakening of Denmark; the renunciation by Holland of all efforts to drive Spain out of southern Netherlands; an enormous increase of the power of France. The question whether Spain would be able to maintain itself as a great power alongside of France led to eleven more years of war between the two states, and was decided, in favour of France, by the Treaty of the Pyrenees. This treaty and that of Westphalia were the basis of the preeminent position of France during the second half of the seventeenth century.