After hearing the news that he was ejected as the superintendent from Marcus Whitman, who recently returned from the United States, Lee went to meet the Board in person to defend himself. Crossing Mexico and sailing up the Mississippi River, Lee reached New York City on 27 May 1844. He found the leadership debating over slavery, which soon led to a schism and the formation of the Methodist Episcopal Church, South. In the meantime, Lee went to Washington D.C. and had conferences with both President John Tyler and Senator Thomas H. Benton to present the land claims of the Oregon Mission. When finally meeting with the Board leadership Lee was able to rectify his position but he wasn't reappointed as superintendent. He opted to raise money for the Oregon Institute, (now Willamette University), a school he helped organize. However while visiting his sister in Stanstead, his health failed, and he died on 12 March 1845. His remains were reinterred at the Lee Mission Cemetery in Salem, Oregon in 1906 alongside the remains of his two wives and infant daughter.