Bowman appears to get emotional near the end of his disconnection of HAL's brain. By the time Bowman's done with this process, he has assimilated his own psychological shadow, as represented by HAL.
To link David Bowman's assimilation of his own shadow to his experience as Jonah in the whale, we refer to Joseph L. Henderson in chapter 2 of Man and His Symbols:
"Dr. Jung has pointed out that the shadow cast by the conscious mind of the individual contains the hidden, repressed, and unfavorable (or nefarious) aspects of the personality. But this darkness is not just the simple converse of the conscious ego. Just as the ego contains unfavorable and destructive attitudes, so the shadow has good qualities - normal instincts and creative impulses. Ego and shadow, indeed, although separate, are inextricably linked together in much the same way that thought and feeling are related to each other.
"The ego, nevertheless, is in conflict with the shadow, in what Dr. Jung once called "the battle for deliverance." In the struggle of primitive man to achieve consciousness, this conflict is expressed by the contest between the archetypal hero and the powers of evil, personified by dragons and other monsters. In the developing consciousness of the individual the hero figure is the symbolic means by which the emerging ego overcomes the inertia of the unconscious mind, and liberates the mature man from a regressive longing to return to the blissful state of infancy in a world dominated by his mother.
"Usually, in mythology, the hero wins his battle against the monster...But there are other hero myths in which the hero gives in to the monster. A familiar type is that of Jonah and the whale, in which the hero is swallowed by a sea monster that carries him on a night sea journey from west to east, thus symbolizing the supposed transit of the sun from sunset to dawn. The hero goes into darkness, which represents a kind of death. I have encountered this theme in dreams presented in my own clinical experience.
"The battle between the hero and the dragon is the more active form of this myth, and it shows more clearly the archetypal theme of the ego's triumph over regressive trends. For most people the dark or negative side of the personality remains unconscious. The hero, on the contrary, must realize that the shadow exists and that he can draw strength from it. He must come to terms with its destructive powers if he is to become sufficiently terrible to overcome the dragon. I.e., before the ego can triumph, it must master and assimilate the shadow."[a]
a. Man and His Symbols. Ed. with introduction Carl G. Jung. London: Aldus Books, 1964. pp. 110-112.
