The teacher said to his student, “Do you have any excuse for coming late to the school, today?”

Option (A) is correct because all the rules are followed by it. There are two errors in the direct speech sentence: first “the” is not required before “school” and no comma is required after “school”. “Today” is rightly changed to “that day” and the use of “whether” is right owing to the presence of the yes/no question word “Do” in the direct speech.