It has direct links with certain songs on Nebraska: the protagonist in "Johnny 99" notes that he has "debts no honest man could pay," repeating a line used by the protagonist in "Atlantic City", and, like the title song, "Johnny 99" is about a murderer — though rather than being a psychopath like the protagonist in the title song, "Johnny 99" is motivated by his economic circumstances.
Ima izravnih poveznica s određenim pjesmama na albumu: protagonist u "Johnny 99" ističe kako ima "dugove koje pošten čovjek ne može otplatiti", ponavljajući rečenicu koju je izgovorio protagonist u pjesmi "Atlantic City", a kao i naslovna pjesma, "Johnny 99" govori o ubojici - no dok je protagonist u naslovnoj pjesmi psihopat, "Johnny 99" je motiviran ekonomskim uvjetima.