The Revolution had not set out to destroy the Catholic Church so much as to nationalise it. The 1790 Civil Constitution of the Clergy made bishops and priests elected officials paid by the state and required an oath of loyalty to the new constitutional order; a majority of bishops and roughly half the parish clergy refused it, splitting French Catholicism into a constitutional church recognised by the state and a refractory church loyal to Rome, with persecution, emigration and, during the Terror, execution falling on clergy on both sides at different points. By the time Napoleon took power in 1799, France had two rival Catholic hierarchies, a large fraction of the population still practising in secret or not at all, and a Papacy that had been driven from Rome twice by French armies.
Napoleon wanted religious peace for practical reasons: an unreconciled Church was a standing source of royalist and counter-revolutionary sentiment, particularly in the west of France, and normal civil life was hard to run without settled parish structures for birth, marriage and death. Negotiations with Pope Pius VII, conducted through intermediaries over many months, produced an agreement signed in July 1801 and promulgated the following Easter, after Napoleon had added, over the Pope's strong objection, a set of unilateral Organic Articles that gave the French state further supervisory power over the Church's public functioning.
The settlement required something genuinely difficult of both sides. Pius VII had to ask the surviving constitutional and refractory bishops alike to resign so that an entirely new episcopate could be appointed jointly, a demand many bishops resisted, and Napoleon had to accept a Church whose loyalty to Rome he could not fully control even as he gained new power over its administration.