The deserters who descend upon southern Illinois are a fearsome bunch, intent on keeping themselves hidden from authorities and subsisting on whatever they can forage in the woods or pilfer from local farms. They are armed, and, in their desperate struggle to survive, create an atmosphere of terror for the Creightons and others who live in the area. It is not long before a murder occurs. A ne'er do well named Hig Phillips, who had avoided the draft by hiring someone to go to war for him, is killed in the dead of night by a band of runaway soldiers. They are furious that he has sat around at home for no reason other than sheer laziness for the past two years, while they have borne the unspeakable burden of war. 

One night in early 1863, representatives from the Federal Registrars come to the Creighton farm hunting down "deserters from the United States Army." They are looking for Ebenezer Carron, who has gone missing from the 17th Illinois Infantry and is believed to be making his way home. Although Matt Creighton asserts that the family has not heard from Eb for some time, the soldiers search the premises. They find nothing, but before they leave, one of them warns Jethro that if Eb should show up, he is to contact the Office of the Federal Registrars in Chicago immediately, or he and his family "will be up to [their] necks in trouble."

Spring comes early that year, and by the first of March, the fields are ready to be plowed. While Jethro is working over at John's place one morning, he hears the repeated call of a wild turkey emanating from the bordering woods. When the boy goes to investigate, he encounters a filthy, skeletal figure: it is Eb, who is indeed a fugitive from the law.

At first, Jethro remembers only that Eb is family, and extends his hand, but the ragged soldier refuses to take it. Eb fully understands his own grave predicament, and knows that the family will get into "awful trouble" if they harbor him. He is ashamed of what he has done, but explains bitterly:

I come because I couldn't help myself...There be things that air too terr'ble to talk about—and you want to see the fields where you used to be happy...you go crazy fer an hour or so—and then you don't dare go back.

Eb had been at Pittsburg Landing with Tom. He recalls that the day before the fateful battle, he and Tom had been "in good spirits...laughin' and carryin' on like...the old days back home." When Tom was killed, something in Eb had died too, and, in a moment of utter despondency, he had made the fateful choice to leave his unit. Now that he is thinking a little more clearly, Eb wishes he could just return to his "old outfit and pitch into the fightin' agin." He would then at least have a chance at survival; as it is, if he returns, or is caught, he will be shot as a deserter. Despairingly, he laments, "There's no place on this earth fer me to go."

Jethro brings Eb some blankets, and smuggles him food whenever he can. Over the next few days, the boy, at only eleven-years-old, wrestles with a moral dilemma that would confound men of far greater age and experience. On the one hand, he knows that by helping Eb, he is endangering his family and breaking the law, but on the other hand, he feels sympathizes with his scared and hopeless cousin. Jethro does not know if he might have done the same thing as Eb similar circumstances, and wonders if "maybe to go on bein' a hero in a war that has no end in sight is too much to ask" of a man. With uncommon maturity, Jethro opts not to consult his father about the matter, because he does not want to put his ailing parent "in the spot where any way he decided would be bad—hurtful to a man's conscience." Finally, with nowhere else to turn, he makes the audacious decision to seek counsel directly from the top, and writes to the nation's president.

Jethro continues to help Eb secretly while he waits for an answer to his letter. The time seems interminable, and all the while, he cannot reveal to anyone what is clearly tormenting him. Finally, one evening, Ed Turner arrives with an envelope from Washington, D.C. The message has been penned by Abraham Lincoln himself, who notes that the problem the boy describes is one that has caused him much agonized consideration as well. In fact, the president had made a decision on the matter just prior to receiving Jethro's letter. Per his decree:

All soldiers improperly absent from their posts, who will report at certain points designated by local recruit offices by April 1, will be restored to their respective regiments without punishment except for forfeiture of pay and allowances for the period of their absence.

The decision for amnesty had been reached after much deliberation, and the president acknowledges that there will be much criticism of his choice. In a show of genuine humility and purity of heart, Abraham Lincoln writes that if his decision is ultimately deemed wrong, at least he has "erred on the side of mercy."