After arriving in Nova Scotia from England in October 1791, Clarkson worked with the Black Loyalist leader Thomas Peters and gathered a group of close to 1,200 African Nova Scotians who wanted to leave for better opportunities in Sierra Leone. Some wanted to return home, having been kidnapped and enslaved from Africa as children. They departed in fifteen ships for Africa late in the year, meeting terrible conditions at sea. After a harrowing transatlantic passage in winter, the flotilla of 15 ships arrived in Sierra Leone in March 1792. The Africans from Nova Scotia, who became known as the Nova Scotian Settlers, established Freetown. Clarkson remained at the settlement until returning to England at the end of December 1792. He served as governor from August 1792 until his departure.