In 1797, the newly promoted General de Brigade Leclerc married Napoleon's younger sister Pauline Bonaparte, with whom he had a child.
After serving in the second unsuccessful French Army military expedition to Ireland led by Jean Joseph Amable Humbert in 1798, Leclerc gained the promotion to general de division, which allowed him to aid Napoleon Bonaparte's bid for power. He participated in the coup d'etat of 18 Brumaire (in November 1799) that made Napoleon First Consul of France. More military campaigns followed on the Rhine and in Portugal.
With a large expedition of warships and a total of 40,000 European troops, the French won several victories after severe fighting. With the tide turning, a number of Louverture's key officers, whom Leclerc promised would maintain their ranks in the French Army, abandoned the old general. L'Ouverture was forced to negotiate an honorable surrender, and he promised to retire to tend his plantations.
Napoleon's secret instructions to Leclerc were to arrest Toussaint L'Ouverture. Leclerc seized L'Ouverture during a meeting and deported him to France, where he died while imprisoned at Fort-de-Joux in the Jura mountains in 1803. L'Ouverture was widely feared in Saint-Domingue and his harsh discipline had made him numerous enemies.
By cleverly playing with the ambitions of L'Ouverture 's younger competitors, Leclerc was close to disarming the Creole officers. News arrived from Guadeloupe that the French expeditionary force sent there had restored slavery. This was what L'Ouverture had always suspected was the reason for the size of the French forces and what he had tried to tell his people.
Slavery had been abolished in Saint-Domingue since late 1793. Leclerc had publicly repeated Bonaparte's promise that "all of the people of Saint-Domingue are French" and forever free. The prospect of the restoration of slavery in Saint-Domingue swung the tide inexorably against French hopes for reimposing control. Creole insurgents again began to fight the French, who were also weakened by an epidemic of yellow fever. Leclerc's reports to France about his counter-insurgency campaign included such statements as, "Since terror is the sole resource left me, I employ it", and, "We must destroy all the mountain negroes, men and women, sparing only children under twelve years of age. We must destroy half the negroes of the plains..." Leclerc died of yellow fever in November 1802. He was succeeded in command by General Rochambeau, whose brutal racial warfare drew more leaders back to the rebel armies, including black and mulatto army officers Jean Jacques Dessalines, Alexandre Pétion and Henri Christophe.