Johnson and Charles Phillips, also of the CMS, arranged a ceasefire in 1886 and then a treaty that guaranteed the independence of the Ekiti towns. Ilorin refused to cease fighting however, and the war dragged on. In 1880, he became a deacon and in 1888 a priest. He was based in Oyo from 1881 onward and completed a work on Yoruba history in 1897. This event is said to have been caused by him fearing that his people were losing their history, and that they were beginning to know European history better. Ironically, this work was misplaced by his British publishers.
After his death, his brother Dr. Obadiah Johnson re-compiled and rewrote the book, using the reverend's copious notes as a guide. In 1921, he released it as A History of the Yorubas from the Earliest Times to the Beginning of the British Protectorate. The book has since been likened to the rise and decline of the Roman Empire by Edward Gibbon.