In March 1781, Warner confronted Ethan Allen, who then publicly admitted to limited contact with the British about prisoner exchange. On May 8, 1775, a council of officers appointed Warner third in command after Ethan Allen and James Easton of Pittsfield, Massachusetts, of an expedition to capture Fort Ticonderoga. In the late summer and fall of 1775, an American army under command of Philip Schuyler and then Brigadier General Richard Montgomery invaded Canada by way of Lake Champlain. By then the British had refortified St. John, and the Americans besieged the fort on the Richelieu River. In mid-September, Warner and his regiment saw action near Fort St. John before being stationed along the St. Lawrence River where they kept watch on Montreal and the British shipping. On the afternoon of July 6, the main body of the retreating army passed through Hubbardton, a frontier settlement about 20 miles from Mount Independence. Following the Battle of Hubbardton, Warner and his regiment guarded the frontier north of Manchester, Vermont, with orders from Schuyler to seize cattle and carriages and to arrest "Tories" (Loyalists). With his health failing, Warner returned to Woodbury where he died on December 26, 1784, at age 41. He was financially insolvent and, except for small holdings for his widow, his property was sold to pay creditors.