Buonaparte led at Schoenbrunn nearly the same course of life to which he was accustomed at the Tuileries; seldom appearing in public; occupied incessantly with his ministers and generals.  The length to which the negotiations with Austria were protracted excited much wonder; but he had other business on hand besides his treaty with the Emperor Francis, and that treaty had taken a very unexpected shape.

It was during his residence at Schoenbrunn that a quarrel, of no short standing, with the Pope reached its crisis.  The very language of the Consular Concordat sufficiently indicated the reluctance and pain with which the head of the Romish church acquiesced in the arrangements devised by Buonaparte, for the ecclesiastical settlement of France; and the subsequent course of events, but especially in Italy and in Spain, could hardly fail to aggravate those unpleasant feelings.  In Spain and in Portugal, the resistance to French treachery and violence was mainly conducted by the priesthood; and the Pope could not contemplate their exertions without sympathy and favour.  In Italy, meantime, the French Emperor had made himself master of Naples, and of all the territories lying to the north of the papal states; in a word, the whole of the peninsula was his, excepting only that, narrow central stripe which still acknowledged the temporal sovereignty of the Roman Pontiff.  This state of things was necessarily followed by incessant efforts on the part of Napoleon to procure from the Pope a hearty acquiescence in the system of the Berlin and Milan decrees; and thus far he at length prevailed.  But when he went on to demand that his holiness should take an active part in the war against England, he was met by a steady refusal.  Irritated by this opposition, and, perhaps, still more by his suspicion that the patriots of the Spanish Peninsula received secret support from the Vatican, Buonaparte did not hesitate to issue a decree in the following words:  “Whereas the temporal sovereign of Rome has refused to make war against England, and the interests of the two kingdoms of Italy and Naples ought not to be intercepted by a hostile power; and whereas the donation of Charlemagne, our illustrious predecessor, of the countries which form the Holy See, was for the good of Christianity, and not for that of the enemies of our holy religion, we, therefore, decree that the duchies of Urbino, Ancona, Macerata, and Camarino, be for ever united to the kingdom of Italy.”

The seaports of the papal territory were forthwith occupied by French troops, but Pius remained for some time in undisturbed possession of Rome itself.  On his return from Spain, however, Napoleon determined to complete his work in Italy, ere he should begin the inevitable campaign with Austria.  General Miollis, therefore, took military possession of Rome in February, 1809; the Pope, however, still remaining in the Vatican, and attended there as usual by his own guards.