Since the catastrophic failure of the original Discovery 1 mission, David Bowman has undergone something of a transformation. No longer an embodied human being he's now a non-corporeal, energy-based life-form. This makes him much like the aliens who control the monoliths.

In his new guise Bowman is able to travel to Earth and make contact with significant people from his past. He visits his mother and brushes her hair shortly before she passes away. He also appears to his former girlfriend on her television screen. Bowman is being used by the aliens who control the monoliths as a probe to learn more about humankind.

After visiting Earth Bowman then heads off to the Jupiter system, where he explores beneath the ice of Europa. There, he finds aquatic life-forms. Under the clouds of Europa he also finds gaseous life-forms. Both the forms of life discovered by Bowman are quite primitive, but the aliens using him see him as having great evolutionary potential.

Later on in the story, Bowman will get the aliens to remove HAL-9000's artificial intelligence from the computer core of the Discovery and transform HAL into the same life-form as himself, the non-corporeal, energy-based life-form that he now is. This will enable HAL to become Bowman's companion.