Juan Rulfo's story is about revenge. It is also, more broadly, about cause and effect. The central theme involves taking responsibility for one's actions and the impossibility of escaping the consequences of harmful actions. One may choose to be harsh or compassionate; both types of actions bring different consequences.
The colonel wants to avenge his father's death. He resents Juvencio for having killed his father, Lupe, many years earlier. Juvencio begs for his life to be spared. The irony involves the decision the colonel must make. Should he exercise compassion and treat this killer mercifully? He knows Juvencio did not behave that way. From the other perspective, the same kind of of irony is played out. Juvencio begs to be treated in the way that he himself refused to act when he took Lupe's life.