To understand why Makar confesses to Aksionov and then to the authorities, it is necessary to know some of the story's background and what leads up to the confession. It is also important to realize that the author, Leo Tolstoy, had a spiritual awakening around the time this story was written and became a devout Christian.

The short story "God Sees the Truth, But Waits" by Leo Tolstoy tells of Ivan Dmitrich Aksionov, a merchant who is unjustly accused of murder and robbery. For his supposed crime he is beaten and then sent off to hard labor in Siberia. He never sees his wife and children again. In his despair, Aksionov turns to God and prayer.

For 26 years Aksionov endures his captivity. He reads holy books, prays, sings, and is renowned for his meekness. The prisoner Makar arrives with some other new convicts, and some remarks that he makes convinces Aksionov that Makar actually committed the murder that caused him to be sent to prison. At first Makar threatens Aksionov, but when Aksionov does not turn Makar in for digging an escape tunnel, Makar confesses to Aksionov that he was the one who killed the merchant and that he had intended to kill Aksionov, too.

Makar confesses to the crime first to Aksionov and then to the authorities because he is touched by Aksionov's sincerity and piety. The only way Aksionov has managed to endure his many years in the labor camp is by developing closeness to God. The purity of Aksionov's character breaks through Makar's initial bluster and lies and causes him to long for the honesty and proximity to God that Aksionov has. Only in this way can he hope for forgiveness not only from Aksionov, but ultimately from God.

Leo Tolstoy could have had Makar Semyonich confess to Ivan Dmitrich Aksionov in order to reinforce the latter’s saintly properties. In other words, Tolstoy makes Makar tell Ivan the truth because it provides clear evidence of Ivan’s honorable character.

After Ivan is wrongly accused of killing the merchant, he’s sent to what appears to be a Siberian prison camp. He starts to read a book called The Lives of the Saints and sing in the church choir. With his long beard and white hair, Tolstoy even gives Ivan the look of a biblical figure. The other prisoners agree. They call Ivan “The Saint.”

Tolstoy then puts Ivan’s saintliness to the test by introducing Makar. The possibility that Makar actually killed the merchant besets Ivan with unchristian thoughts, like vengeance. However, when Ivan has the chance to tell on Makar and get him flogged, he abstains.

Ivan’s refusal to play a part in Makar’s punishment—a punishment that might prove deadly—enhances his saintly credentials. The reader sees the extent to which Ivan is dedicated to God and the value system that he has created for himself. Ivan is such an upstanding person that he passes up the chance to punish someone whose actions have destroyed his life.

Makar’s final confession puts the finishing touches on Ivan's character development; it cements the notion that Tolstoy has created someone who could reasonably be called a saint.

Ivan Dmitrich Aksionov, a once respectable businessman, is now a prisoner in a wretched Siberian penal colony. He was sent there after being wrongly convicted of the murder of a merchant, who was brutally stabbed to death while staying at the same inn as Aksionov. Though Aksionov always protested his innocence, the authorities didn't want to know about it, and so this innocent man would rot away in prison for decades.

One day, when a new batch of prisoners arrives, Aksionov recognizes someone from his own town. The man, called Makar Semyonich, seems to know Aksionov, too. Before long, Aksionov suspects that it was Makar who murdered the merchant all those years ago, a crime for which he was wrongly convicted.

Even so, when an escape tunnel dug by Makar is discovered by the prison authorities, Aksionov doesn't try to get revenge by informing on Makar, even though he knows full well that Makar was responsible for digging the tunnel.

Makar is so moved by Aksionov's actions that he begs the old man's forgiveness and confesses to the killing of the merchant. Although there's no doubt that Makar has been genuinely moved by Aksionov's refusal to get him into trouble with the prison authorities, there's an element of quid pro quo about his confession. Aksionov has done him a favor, so he will do him one in return.

"God Sees the Truth, But Waits" is the story of a man, Ivan Dmitrich Aksionov, who is imprisoned in Siberia for over twenty years for a crime he did not commit.

He tries to make the best of his life as a falsely imprisoned man. He devotes his life to God and becomes a friend and confidant for the other prisoners and the prison guards.

Some prisoners, including Makar Semyonich, are transferred from another facility. As he hears them talking amongst each other, Aksionov becomes convinced that Semyonich is the man responsible for the crime he is accused of committing. But he keeps this information to himself.

Semyonich attempts to dig a tunnel that will free him from the prison. The guards discover it and question Aksionov about it, but he refuses to tell them what he knows—partially out of fear of Semyonich, but also out of a lack of certainty that he actually saw what he thought he saw. Semyonich is so moved by Aksionov's act of protection that he freely admits to killing the merchant—both to Aksionov and the authorities. This leads to Aksionov being cleared of all charges, but he dies before he is released.