| Operational | Commander | Type | Non-operational | Type |
| Cheyenne Mountain, CO | General Sebastian Monroe | Main Militia Headquarters | Crosby, MS | Training Base |
| Philadelphia, PA | AC Captain Burke | Eastern Headquarters | Southern Illinois | Scouting/Training/Regular |
| Austin, TX | General Blanchard | Southern Joint TX/Militia Headquarters | Las Vegas, NV | Scouting |
| Springfield, IL | Captain Stan Taylor | Midwest Militia Headquarters | St. Marys, OH | Regular/Front |
| Durango, CO | General Miles Matheson | Outbase/Specialized Training | West Viginia | Scouting |
| Schriver AFB, Colorado Springs, CO | General Miles Matheson | Research and Development | Port Heron, MI | Training/Port |
| Southern South Dakota | Regular | AC Major Lewis | Salt Lake City, UT | Specialized Training/Outpost |
| Sulphur, LA | Major Jason Neville | Research and Development | St. Petersburg, FL | Port/Ship Building |
| Monroe, LA | Regular/Training | Lt. General Charlie Matheson | Fort Kent, ME | Regular/Training/Undercover Operations |
| Las Cruces, NM | General Jeremy Baker | Regular/Hot Weather Training | Branson, MO | Regular/Interrogation |
| El Paso, TX | Lt. Wilson | Training | Jonesboro, AR | Medical Base/Training |
| Dallas/Ft. Worth, TX | Captain Robinson | Liaison Base, TX/Monroe Republic | Kansas City, KS | Emergency Site for Generals Monroe and Matheson |
| Flagstaff, AZ | Captain King | Terrain Training | Augusta, ME | Surveillance/Port/Training |
| Ft. Carson, CO | General Sebastian Monroe AC General Hansen | Training/Medical |
| Henderson, NV | Lt. Turner | Research and Development |
| Carbondale, IL | Captain Mitchell | Regular Base/Special Operations |
| Marion, IL | Lt. Col. Evans | Regular/Disciplinary/Prison |
| Cheyenne, WY | Captain Nichols | Regular/Training |
| Lincoln, NE | Major Stone | Regular/Transportation |
| Little Rock, AR | Captain Blackstone | Regular |
| Pierce, ID | Major Norman | Training |
| Picatinny Arsenal, NJ | Lt. Col. Larson | Weapons Depot/Weapons/Special Forces Training |
| Lake of the Woods, MN | Major Cook | Training/Intelligence/Guerilla Warfare |
| Homestead, FL | Captain Harrison | Housing/Port/Ship Building |
