Greene was appointed a captain in the Missouri State Guard in 1861, and was sent by Jackson along with Capt. Basil W. Duke to Montgomery, Alabama, (then capital of the Confederacy) to ask the recently elected Confederate President Jefferson Davis for artillery. It was hoped this could be used to attack the Federal arsenal in St. Louis, however the captains arrived with their artillery too late to help in the effort, and the cannon were captured by Union troops. Despite this setback, Greene soon afterwards aided Gov. Jackson to drill recruits that had gathered in Jefferson City, as well as missions that summer into Arkansas and to Richmond, Virginia, to seek support for invading and reclaiming Missouri, now increasingly under Union control.