The story begins more than eight years before any other Sin City book takes place, with policeman John Hartigan on his final mission before his forced retirement (he has severe angina). Roark Junior, son of one of the most powerful and corrupt officials in Basin City, is indulging his penchant for raping and murdering pre-pubescent girls. It is Hartigan's mission to rescue Junior's latest quarry, an 11-year-old named Nancy Callahan.
Hartigan succeeds in rescuing Nancy by disabling Junior's getaway car, which was being guarded by Burt Schlubb and Douglas Klump, two guns-for-hire with "delusions of eloquence". Hartigan knocks them out and kills the twin guards Benny and Lenny. He chases the escaping Junior to the pier and then proceeds to use his revolver to surgically shoot off Junior's left ear, right hand, and genitals. Before he can finish Junior off, Hartigan's corrupt partner Bob, who fears angering Senator Roark, shoots Hartigan several times. Hartigan then stalls Bob for as long as he can to save Nancy when backup arrives, going so far as to pull a spare gun and have Bob unload his gun on him. Bob leaves the fallen Hartigan, who passes out with Nancy in his arms.
Roark Jr. lapses into a coma from his injuries, and Senator Roark takes issue with the abuse of his son. Hartigan survives and recovers thanks to the senator, who wants Hartigan to suffer for the rest of his life. He is framed for raping Nancy, branded as a pedophile and sentenced to a lengthy prison term amid a public outcry that brands him one of Sin City's most hated citizens. He remains silent about his pain, knowing that Senator Roark would execute anyone who ever found out the truth. The only one to whom Hartigan speaks in the hospital is Nancy, who sneaks out against her parents' wishes to see the man who saved her. Hartigan tells her to stay away from him, so Nancy tells Hartigan she will write him letters instead. She will sign her name as "Cordelia" to hide her identity. Before leaving, Nancy tells Hartigan she loves him.
After his stint in the hospital, Hartigan is seen tied to a chair, cuffed and being beaten by Det. Liebowitz in order to force him to sign a false confession. Amid the hours of repeated punching and being tempted by prison luxuries and even sex with an Old Town prostitute, Hartigan doesn't crack under the pressure, although he hallucinates that he is granted the strength of Hercules, breaks from his cuffs and kills Liebowitz by exploding his head.
Afterwards, alone in prison and abandoned by his wife Eileen (who remarries and finally has children) and his friends, he finds solace in the carefully disguised weekly letters he receives from Nancy. Hartigan quickly develops a paternal love for young Nancy, and sees her as the daughter he never had. For eight years, he drags himself through his jail time, his only respite the letters his young admirer sends him, until finally the letters stop coming. Although he initially believes Nancy has merely outgrown her childhood hero, Hartigan soon becomes increasingly worried that Senator Roark has finally found her. His fears are confirmed when a deformed, hairless visitor with sickly yellow skin who smells distinctly like garbage arrives at his prison cell and punches him out. Hartigan awakens and discovers the same type of envelope Nancy always uses containing an index finger from the right hand of a 19-year-old girl.