Aomame is a fitness trainer and assassin living in Tokyo, Japan, in 1984 who targets abusive men. While enroute to an assassination, she gets stuck in traffic and takes an emergency stairwell off an expressway to save time. She has unwittingly entered a parallel world, which she calls 1Q84 (Q standing for "Question) because she seems to have lost track of time and her understanding of reality has become skewed.

Tengo is an aspiring writer who knew Aomame when they were children. Tengo has undertaken the assignment to rewrite the short story "Air Chrysalis" by seventeen-year-old writer Fuka-Eri. Tengo's committal to rewrite the story to make it acceptable for publication also plunges him into 1Q84, which is what Fuka-Eri wanted. Fuka-Eri herself is a msyterious person, whose family is involved with a religious cult called the Sakigake. The Sakigake believe that their leader hears voices from beings known as the Little People. Fuka-Eri's father is the leader and is Aomame's next assignment for having raped Fuka-Eri when she was younger.

Before being killed, the Leader explains to Aomame that she is indeed in a parallel world of sorts where nothing truly makes sense. He explains he hears voices, and that the Little People have tremendous power which when exercised, must be balanced by a reactive force. Fuka-Eri's story exposes the Little People, and puts a check on their power. Tengo, whose own creative powers have been freed by working on rewriting "Air Chrysalis," is also writing his own novel which is a further safeguard against the power of the Little People. When Aomame kills the Leader, she becomes pregnant with Tengo's child, who the Little People seek to use as a replacement for the Leader.

Tengo and Aomame search for one another, for they realize they are connected in the plot of the Little People, and they both return up the ladder to the expressway (with Tengo holding onto his own novel in manuscript form) and leave 1Q84.