The Consolidation - the West
"...
an insect of a man, who with a stroke could have felled an elephant..."
- Joseph Bonaparte
Napoleon's near-death experience in Rome hardened his resolve against his enemies and perhaps helped end his giddy sense of indestructibility that had followed him since the improbable rout at Austerlitz. His goal now was one thing, and one thing alone - to consolidate his victories and set up the new France for his great dynasty. He was still in Rome, drafting his next decisions, when he heard that Talleyrand had secured Grand Duchess Catherine of Russia's hand in marriage. Napoleon was elated at the diplomatic stroke though saddened that he would have to bid farewell to his beloved, but barren, Josephine.
The news perhaps was well timed, for it helped satisfy the Emperor enough that his redrawing of Italy's map in the summer of 1809 was milder than expected. His sister Elisa and her husband Felix, already Prince and Princess of Lucca and Piombino, were now granted titles as Queen and Prince Consort of Etruria, which was to see its French occupation ended, but its position in the Continental System maintained, now that Charles Louis had been compensated as Charles II of Portugal. Napoleon quietly granted the Kingdom of Italy some of Bavaria's land south of the Alps (and the city of Trent) in return for ceding his personal possessions of Bayreuth and Erfurt to Maximilian Joseph, and then set about attempting to solve the question of Rome.
The reality was that with the Peace of Stockholm guaranteeing, at least for the time being, a broad peace on the land and much of his armies headed home for a much-needed rest from war, the necessity and costs of garrisoning Italy were starting to look daunting. Not only that, but Napoleon had two siblings now in Florence and Naples, a personal union with the Kingdom of Italy in the north which would eventually go to his adoptive son Eugene de Beauharnais, and in the Papal State a Pope, Pius VII, who participated willingly and openly in the Continental System. Napoleon saw Rome as the ultimate feather in his cap, however; it was his desire to incorporate it into his personal domain and to make his and Catherine's future son titular King of Rome. That Pius VII had been insufficiently responsive to the near-assassination by that damned priest irked him as well.
It was Bernadotte who, in one of his lengthy debates on geopolitics
[1], presented a solution to Napoleon. Knowing that the Papacy would not accept a complete suspension of temporal powers in the Papal State, he instead suggested incorporating it as a "protectorate." In the Farnese Declaration, made from the Palazzo Farnese, Napoleon announced that France would heretoforth regarded the Papal State as its protectorate, with the French Emperor "defender of the Church" by title. In his role of Defender of the Church, France would be wholly responsible for the Church's temporal (though not spiritual) activities of foreign policy and defense, meaning that the army of the the Papal State would be under direct French control. Internally, the Papal State would be governed by the Curia as before; however, the French Emperor was permitted to grant noble titles within its territory, and as his first move named Bernadotte Duke of Anzio (and thus his titular personal representative in Rome) in addition to his title as Prince of Pontecorvo, and vowed to make "Duke of Rome" the title of his heir. The Duchy of Rome, though holding no temporal authority, was to enjoy substantial incomes for which the Pope would be responsible to produce; several cardinals noted begrudgingly that this reeked of France extorting the Papacy at gunpoint, perhaps not an inaccurate summation of the state of affairs.
The more fundamental reason Napoleon did not annex Rome entirely, of course, was not just to avoid setting Catholic Europe aflame in anger (particularly Austria, which would be sure to react to such a move what with its substantial army reforms over the last four years) but to avoid any distractions from his final target - Britain. The Farnese Declaration, though reviled in Italy and stirring up a great deal of resentment in the Papal State, was the exclamation point on European peace in Napoleon's mind. "The matters of state here have been solved," he announced. Now only Britain remained, with all other enemies conquered or sated. In Italy in particular, his able brother Joseph had in a few short years turned Naples into a model kingdom, doubling the number of roads and schools while the reactionary Bourbons he had overthrown sulked in Messina in Sicily licking their wounds and glaring angrily. A new, enlightened cadre of monarchs dotted the continent now, upholding Napoleonic ideals. But Britain remained to fend off, and Napoleon needed a lasting peace to defeat the enemy he obsessed over the most. Later in 1809, with his Army of the Low Countries, he stood at Calais and stared across at the White Cliffs of Dover, thinking about what he would need to achieve to find victory over London...
[1] Hat tip to
@alexmilman for this idea