The Shaw family live on a remote farm. They face upheaval when a deadly virus takes hold worldwide, devastating life as they know it. One by one the family succumb to the infection, apart from 17-year-old twins Kerryl and Lander. The companion book Paradise Girl tells the progress of the infection through Kerryl's diary, and what happens to her. Aftershocks is the story of her brother, Lander, who leaves the farm at an early stage.

He is looking to join a group he has met on the internet, who have theories about the infection and its aftermath. Emergency regulations have banned travel, so he realises that he must avoid government patrols. However, these are not the worst of the threats he faces. He is gassed, caught, put on trial and imprisoned. Mysteriously he is taken from prison to a medical facility, where he finds people who want to experiment on him. He escapes from there to encounter a woman and her son, who face him with a terrible choice. He moves on to find help and temporary safety in the home of an old lady who treats him like a son. He is tempted to stay but he moves on, only to be captured by a cruel and unscrupulous character who uses him as a slave.

He is freed from there by a fellow slave, Magda, and together they return to Lander's home, where he finds that Kerryl is dead and the farmhouse is occupied by one of her friends, Steve. Lander decides to head south to find Adam, the man he blames for Kerryl's death, and he, Magda and Steve set out, using the canal system to avoid travelling by road and encountering government patrols.

Part way on their journey they meet Lisa, who is looking for a group of women who have formed a commune after the plague. They locate the group in an old manor house, but while visiting there Lander sees the man for whom he is searching. There is a confrontation and a fight, stopped by the intervention of Magda. It transpires that Magda and Adam are in league, and they try to persuade Lander to help them in their plan to manage the future. However, Lander cannot forgive Adam for what he did to Kerryl, or Magda for deceiving him. He abandons them to continue his search for people he can trust and who will help him build the brave new world he is sure is possible.