Klara and the Sun takes place in a near-future society where technology has advanced significantly. In this society, where social and safety constraints often engender loneliness among school-age children, it's common for families to hire an "AF," which stands for "Artificial Friend"—an artificially intelligent solar-powered being calibrated to provide exemplary companionship. The story is narrated from the first-person perspective of Klara, an extremely perceptive AF.

Klara is friendly and well-liked, and enjoys a special relationship with the Sun, whom she views as a sentient being generously sharing nourishment to keep AFs alive. When she sees a man revived in the sun across the street from the window of the store where she lives, she comes to believe the Sun can bestow this healing nourishment on humans at will, too. After the sun's rays are blocked out for several days by pollution from an industrial machine, Klara begins to view the machine—“the Cootings Machine," named for the "Cootings" logo on its side—as a sinister emblem of darkness, in the Sun's direct opposition.

After a long, patient wait at her department store, Klara is finally chosen. She's purchased by a teenage girl named Josie Arthur and her mother, whom Klara refers to as simply "the Mother." Josie is vivacious and smart, but she's also suffering from a mysterious ailment that occasionally renders her bedridden.

As she acclimates herself to living at home with the family, Klara begins to develop a more nuanced view of the relationships between human beings. For the first time, she learns about the complicated relationships between people who love each other and the fragile tension that can exist between mothers and daughters. Soon, she learns that Josie and Rick, the boy next door, are romantically involved, and is able to observe this different kind of love, too.

After witnessing Josie and Rick around their peers, however, Klara realizes that some human behavior may be more complicated. Josie, like most teenagers, has been "lifted," while Rick has not. This means that Josie has been given advantages that make her more likely to excel, but the lifting process also comes with risks. As the narrative progresses, it becomes clear that complications from the lifting process have caused Josie's sickness. Eventually, Klara learns that Josie once had a sister, Sal, who died under the same conditions.

Josie's health begins to waver, and Klara soon becomes certain that the only way to cure her is to beg assistance from the Sun. He's previously shown himself capable of curing human illness by reviving the beggar outside the department store, she reasons. Remembering that he appeared to set upon a barn she can see from Josie's window, Klara asks Rick to help her find the barn. On arrival, she proposes a bargain: she'll disable the Cootings Machine so it can no longer spew darkness and pollution if the Sun will help Josie.

Klara is invited along to an appointment in the city, where the Mother is having a mysterious portrait of Josie done. Josie's father, a former engineer whom Klara calls "the Father," joins them in the city. At the portrait appointment, it's clear that something is amiss—Josie thinks she's having a painting done, but Mr. Capaldi, the "artist," is actually building an AF replica. Klara, he's hoping, will be able to take over as a replacement for Josie if Josie should succumb to her illness. Artificial intelligence has advanced far enough that it should no longer matter, he argues—there's nothing inside a human that an AF can't authentically replicate.

An argument ensues, and the family leaves to calm down. Klara, having spotted the...