The remarks about the soul being the prison of the body reflect Foucault's love of contradictions, but they also make a deeper point. The body is imprisoned because people can be controlled by sciences directed at the soul, such as psychiatry. Foucault attempts to chart a move from a situation where the criminal's body is attacked, to one where we are all disciplined and controlled.
Finally, Foucault's role in the prison reform movement is an important context for this section: he helped to run the French Groupe d'information sur les Prisons (GIP) in the 1970s. The group distributed information on prisons to the public, and was concerned with letting prisoners speak for themselves. In a way, Foucault sees Discipline and Punish as a theoretical counterpart to the work he carried out in practice.