The novel's protagonist, Iris Chase, and her sister Laura, grow up well-off but motherless in a small town in southern Ontario. As an old woman, Iris recalls the events and relationships of her childhood, youth and middle age, including her unhappy marriage to Toronto businessman Richard Griffen. The book includes a novel within a novel, the eponymous Blind Assassin, a roman à clef attributed to Laura but published by Iris. It is about Alex Thomas, a politically radical author of pulp science fiction who has an ambiguous relationship with the sisters. That embedded story itself contains a third tale, a science fiction story told by Alex's fictional counterpart to the second novel's protagonist, believed to be Laura's fictional counterpart.
The novel takes the form of a gradual revelation illuminating both Iris's youth and her old age before coming to the pivotal events of her and Laura's lives around the time of the Second World War. Laura and Iris live in a house called Avilion. Their mother dies at a young age leaving Reenie, the caretaker, to take on responsibility for the girls. As the novel unfolds, and the novel-within-a-novel becomes ever more obviously inspired by real events, Iris, not Laura, is revealed to be the novel-within-a-novel's true author and protagonist. Though the novel-within-a-novel had long been believed to be inspired by Laura's romance with Alex, it is revealed that The Blind Assassin was written by Iris based on her extramarital affair with Alex. Iris later published the work in Laura's name after Laura committed suicide upon learning of Alex's death in the war.
Following the suicide, Iris realizes through her sister's journals that Richard had been raping Laura for much of their marriage, blackmailing her to comply with him by threatening to turn Alex in to the authorities. Iris takes her young daughter Aimee and flees her home, threatening to reveal that Richard had impregnated Laura and forced an abortion on her. This move estranges Iris from the last people who were supporting her, and creates bitterness between her and the grown Aimee. Iris deceives Richard into believing that Laura was the one having an affair with Alex Thomas, which drives him to commit suicide. The novel ends as Iris dies, leaving the truth to be discovered in her unpublished autobiography that she leaves to her sole surviving granddaughter.
