The army issued a warrant for my husbands arrest for desertion, what will happen?

My husband was attending AIT through the Army, he hasnt graduated from AIT, or gotten any orders. He has went AWOL twice, but recently his commander told him to go home, because he was being separated from the military. But he didn't fill out any paper work. So we left the state to go home, and he was arrested, because the Army issued a warrant for his arrest for desertion. He will be sent to Fort Knox to be out processed, but what will happen to him? Can he get a lawyer and fight this? I need to know what will happen.