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There might be more than one atonement with the father for each of the characters. For *Butch,* atonement with the father occurs in Maynard's shop, when he rescues Marcellus from the rapists. In so doing, he reconciles with Marcellus, who stands in for the father, representing the punitive, wrathful side of one's own subconscious. Marcellus in effect forgives him for his sins, reducing his sentence from death to mere exile from LA. Hence, he rides away on a motorcycle called "Grace." He is reunited with his feminine aspect in the form of Fabienne, and freed to return home to Knoxville with his newfound wealth.
Perfectly possible for each character to have an atonement. Whether it applies here, I'd need to watch the movie again :)