Primarily, there are two ways that deserters and those who are AWOL are returned to military control: they either return voluntarily, or they are apprehended by the military or civil law enforcement and then transported back to the military.
Each of the services have different policies about where returnees are sent for processing following their return to military control.
Army procedures are contained in Army Regulation 190-9 - Absentee Deserter Apprehension Program And Surrender Of Military Personnel To Civilian Law Enforcement Agencies. Soldiers who took absence from a training unit are returned to the Personnel Control Facility (PCF) at Fort Knox, KY or Fort Sill, OK. Those who have left operational units in the continental United States are returned to the unit from which they took absence. Soldiers in transit from overseas are no longer considered to be assigned to the gaining unit, and will be returned to the PCF at either Fort Knox or Fort Sill.
In the Air Force, (under Air Force Instruction 36-2911 - Unauthorized Absence, if the member has been absent for less than one year, they are returned to the unit they went absent from. If absent for more than one year, they are sent to the nearest Air Force installation which have the capabilities to process AWOL and desertion.
Navy procedures are included in the Navy Personnel Manual ( MILPERSMAN 1600-030 ). Sailors absent for 119 days or less, will normally be returned to their original duty station from which they deserted. Deserters absent for 120 days or more will be returned to the Navy Transient Personnel Unit (TPU) closest to the point of apprehension/surrender. (Note: there are some exceptions to these rules, such as when one goes absent overseas and then surrenders or is arrested in the states.) The Navy TPUs are: TPU, Puget Sound, Sliverdale, WA; TPU, Jacksonville, FL; TPU, Great Lakes, IL; TPU, Norfolk, VA; TPU, San Diego, CA; and TPU, Pearl Harbor, HI.
In most cases, Marines who have been absent for 180 days or less are returned to their parent unit. Male Marines who have been absent for more than 180 days are transported to MCB Quantico; MCB Camp Lejeune; MCB Camp Pendleton; MCAS Cherry Point; MCAS Miramar; MCRD/ERR Parris Island; or MCRD/WRR San Diego (whichever is the closest to the point of apprehension/surrender). Female Marines who have been absent for more than 180 days are assigned to MCAS Miramar. There are a few exceptions to these rules, which can be read in Table 5-1 (page 5-22) in MCO P5800.16A, The Marine Corps Manual for Legal Administration.
Coast Guard procedures are contained in the Coast Guard Personnel Manual , Chapter 8c. In the vast majority of cases, absent Coast Guard members are returned to the command they went AWOL from, upon return to military control. If the unit doesn't have the proper facilities (such as a confinement area), then the District decides where the Coast Guard member is returned to.
More About AWOL and Desertion

