FONTAINEBLEAU, France — The single line of Napoleon’s secret code told Paris of his desperate, last order against the Russians: “At three o’clock in the morning, on the 22nd I am going to blow up the Kremlin.”

By the time Paris received the letter three days later, the Russian czar’s seat of power was in flames and the diminished French army was in retreat. Its elegantly calligraphic ciphers show history’s famed general at one of his weakest moments.

“My cavalry is in tatters, many horses are dying,” dictated Napoleon, the once-feared leader showing the strain of his calamitous Russian invasion, which halved his army....