The novel has two chronological tracks. In one, some terrible catastrophe has occurred, wiping out virtually all human beings. We get the point of view of one, perhaps the only, surviving human, Snowman, who devotes himself to scavenging food, avoiding predators, and looking after the "Crakers," a small community of new, improved humans with DNA re-engineered by Snowman's brilliant but now dead friend, Crake.
In the other, we get Snowman's memories of the pre-catastrophe world. He was then Jimmy, and grew up in a compound -- some kind of autonomous corporate city-state, a kind of armed-&-gated suburb, devoted to bio-tech research and production of consumer goods for the "pleeblands," that is, those parts of the world that are not compounds -- these parts being dirty, dangerous, toxic, a non-stop bazaar where all is for sale, but where there are also occasional gestures of resistance to the power of the compounds. In good speculative fiction fashion, this world is a terrifying extrapolation of our own, with all checks on global capitalism removed, its tendencies to social stratification and environmental degradation utterly triumphant.
It is in the compounds that young Jimmy meets Crake, whose brilliance as a DNA-magician later lands him at the top of a corporate pyramid. Crake plucks his boyhood friend from obscurity to a plum job at his compound, where they both become involved with the beautiful and mysterious Oryx, former child-porn star, currently goddess-figure-cum-tutor for the new, improved humans Crake has designed.
Atwood's deft handling of the two then-&-now narrative time-lines (which reminded me of my favorite among her novels, Alias Grace) places the revelation of the nature of the catastrophe at novel's end. It's a doozy. Crake has come up not only with a species of new Adams and new Eves, programmed to avoid our worst mistakes, but also with the means to wipe the slate, to cleanse the world and ready it for their emergence.
In the closing pages, Snowman/Jimmy has a Crusoe-on-the-beach moment, discovering the presence of other old-model humans like himself. So he locates one of the last of the old weapons and heads out to kill them -- an act of evil undertaken to preserve the innocence of the Crakers. At which point one can only think, here we go again.