A new group of French commissioners appointed Toussaint commander in chief of all French forces on the island. From this position of strength, he resolved to move quickly and decisively to establish an autonomous state under black rule. He expelled Sonthonax, the leading French commissioner, who had proclaimed the abolition of slavery, and concluded an agreement to end hostilities with Britain. He sought to secure Rigaud's allegiance and thus to incorporate the majority of mulattoes into his national project, but his plan was thwarted by the French, who saw in Rigaud their last opportunity to retain dominion over the colony.

Once again, racial animosity drove events in Saint-Domingue, as Toussaint's predominantly black forces clashed with Rigaud's mulatto army. Foreign intrigue and manipulation prevailed on both sides of the conflict. Toussaint, in correspondence with United States president John Adams, pledged that in exchange for support he would deny the French the use of Saint-Domingue as a base for operations in North America. Adams, the leader of an independent, but still insecure, nation, found the arrangement desirable and dispatched arms and ships that greatly aided black forces in what is sometimes referred to as the War of the Castes. Rigaud, with his forces and ambitions crushed, fled the colony in late 1800.

After securing the port of Santo Domingo in May 1800, Toussaint held sway over the whole of Hispaniola. This position gave him an opportunity to concentrate on restoring domestic order and productivity.