It all begins when Ali goes for a checkup in El Cielo.

"Gene and Ali," illustrated by Julius Tabiolo, introduces several major plot threads. The solar fields of Hiawatha, Y Control and Fragile Y Syndrome, concern about the water supply and the algae ponds first appear in this chapter.

Gene Waterman and Ali Rugosa discover that they have conceived a child. What could be a potentially joyful event turns sour when they learn the child is a boy, which makes Gene a carrier of a stable Y Chromosome. To escape agents of Y Control, they must go on the run to protect their freedom. It is followed by "The Paper Score."