It follows the usual black and white noir style artistry of previous Sin City novels, with the exception of yellow on Roark Junior late in the story.
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 suffers from 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.
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".
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.
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.
Believing Nancy to be in imminent danger, Hartigan decides to find some way out, and contacts his lawyer, Lucille (the lesbian parole officer from The Hard Goodbye).
Senator Roark used his vast financial resources to resurrect his son using new medical techniques to re-grow his severed body parts.
Junior knocks Hartigan down, attempts to hang him naked with a noose, and boasts of raping and killing dozens of girls over the past eight years.
At first, Hartigan resigns himself to death but, in a sudden bout of determination, he revives himself through sheer will, breaks a window and cuts his hands free with a glass shard.
Hartigan takes down four other corrupt police officers guarding the Farm and confronts Junior, who by that time has Nancy at knife point.
In the DVD commentary, Frank Miller indicated that he was initially motivated to write That Yellow Bastard after his disappointment with The Dead Pool, the fifth and final film in the Dirty Harry series.