The Genocides describes the genocide of humans by aliens who seed Earth with enormous crop plants. The Plants are massive and rapidly out-compete terrestrial flora, forming a monoculture. They appear unwholesome to the native fauna, and starvation seems inevitable.
The novel opens with a small rural community struggling for survival on the border of Lake Superior. Urban society appears to have collapsed by this point. The community, led by Anderson and his family, eke out an existence by siphoning sap from the Plants to irrigate their corn crop. Anderson is a conservative and religious man, harsh and uncompromising. His focus on survival has kept the community alive long after many have died. His rules include the harsh treatment of outsiders who are routinely killed unless they are of use to the community.
Newcomers arrive bringing with them news of spherical machines that are incinerating every trace of humanity left on Earth, including burning the abandoned cities and remaining survivors. Most of the newcomers are killed and, the novel implies, ground into sausage meat and consumed. The two remaining have useful skills: Alice is a nurse and Jeremiah a mining engineer.
Jeremiah vows a personal revenge on Anderson and his family, but begins by ingratiating himself in the community. Jeremiah courts Anderson's thirteen-year-old daughter, Blossom. He befriends Anderson's educated son, Buddy.
During the harsh winter, the spherical machines come to incinerate the community. Jeremiah sees his revenge coming to fruition. Those who survive the initial conflagration flee into a cave. There they discover the Plants' roots are hollow and form a massive and interlocking underground network. Jeremiah suggests they go deeper, pointing out that they will be able to escape the winter underground.
They discover the "fruit" of the plants is housed in the root system: a nutritious pulp the community begins to consume. Anderson, who lost his wife Lady when fleeing, is weakened. When he is bitten by a rat, gangrene sets in and he declines quickly. His final words to his brutish son, Neil, are to let Jeremiah take over leading the community and to allow Jeremiah to marry Blossom. Neil is angered by these words, and murders Anderson. The nurse Alice sees the signs of murder on Anderson, but Neil murders her before she can share her revelation. The community breaks up.
Jeremiah goes in search of Blossom, planning to kill her when he finds her and commit his ultimate revenge. When he does find her, he experiences a change of heart and falls in love. They try to return, but find Neil has sabotaged their escape and his own. In the dark they cannot find their way back.
Neil, Jeremiah, Blossom and Buddy struggle underground. Neil is overcome and abandoned in the dark.
When the few survivors return to the diminishing group, they find machines have come to harvest the Plants' crop. Without the pulp to live on, the survivors return to the surface.
On the surface it is spring, and a new crop of Plants have been sown by the mysterious aliens. The malnourished group has no chance of survival, and the novel closes on the Jeremiah and Blossom leaving the few other survivors to travel into the wilderness. The pair, starving and mismatched in age, are portrayed as a distorted mirror image of the biblical Adam and Eve and herald the end of humanity instead of the beginning.