Yvon Beaudoin fills in the background for us:
On May 1, 1804, Napoleon succeeded in having the Senate bestow upon him the title of hereditary Emperor of the French. For all intents and purposes, he re-established the monarchy that the Revolution had destroyed. At the time, he was so popular that by means of a plebiscite the people approved the vote of the Senate. The feasts of consecration and of crowning in the presence of Pope Pius VII on December 2, 1804 were carried out with solemnity. The Emperor took up residence at Les Tuileries and held court there like the kings of old.
When Napoleon came to power, he accommodated the Church, but controlled it for his own purposes. It was during this period that Eugene became a seminarian in Paris.
The relations between Rome and Paris were good for a few years. But, having defeated several coalitions, Napoleon wanted to impose the Concordat on all countries where he held sway, especially in Italy, Austria, Belgium and Holland. The Pope opposed this, refusing at the time to grant canonical recognition to the new bishops and by so doing practically rendered the Concordat inoperative. The French troops then seized Rome and the Pontifical States were annexed to the Empire by a decree of May 17, 1809. Pius VII, without mentioning Napoleon by name, excommunicated all those who took part in this action. The Pope was subsequently brought to Savona, Rivière de Gênes, where he stayed for four years and the Italian cardinals were dispersed as far away as Paris. http://www.omiworld.org/en/dictionary/historical-dictionary_vol-1_n/867/napoleon-i/
Eugene learnt to work clandestinely for the cause of the imprisoned Pope, who had excommunicated Napoleon, whom Eugene referred to as “the abominable tyrant, enemy of everything that is good.”
In July of 1808. Pius VII responded to these vexations by a bull of excommunication. But Napoleon forbade its publication in France. Mr. Émery succeeded in getting his hands on a copy and had it transcribed by Abbé de Mazenod to have it subsequently distributed in France. From that time until June of 1810 when Napoleon forced Mr. Émery to leave the seminary, Eugene was a member of the committee dubbed the orium where in the greatest secrecy, documents issued by the Pope or certain cardinals were transcribed. They were then distributed throughout France by trustworthy individuals. If they were taken in flagrante delicto , these volunteer scribes were liable to very severe penalties.