In a plot that spans millennia, the story focuses on the interconnected lives of several characters, including a boy whose special ability may hold the key to unlocking the secrets of the universe.

Fumiko Nakajima is a scientist who designs space stations for a massive business conglomerate called Umbai.

On the resource world Umbai-V, a young boy named Kaeda meets Captain Nia Imani.

Fumiko, having lived almost a millennium with the assistance of cryogenic sleep, hires Nia to care for the child.

Fumiko believes he possesses the ability to Jaunt, meaning to travel through space instantaneously and without time dilation.

Nia and her crew agree to raise the boy for fifteen years outside of the knowledge of Umbai, waiting to see if his powers will manifest.

For fifteen years, Nia travels the universe and plays her music for Ahro, but he does not wake from his coma.

A review in Strange Horizons describes the Umbai corporation as neocolonialist; it profits from the natural resources of worlds such as Umbai-V, yet prevents their inhabitants from participating fully in interstellar society.

Club noted was a "blunt metaphor", the Umbai company powers their FT drive with Ahro's blood.

The first section of the novel is divided into chapters with different protagonists; they could be viewed as a work of related short stories.

In the second part of the novel, the seemingly unrelated fragments are linked together by the lives of Nia Imani, Ahro, and Fumiko Nakajima.

Di Filippo praised the evocative worldbuilding and lush prose, comparing it positively to the works of Samuel R. Delany and Ursula K. Le Guin.

[7] In a starred review, Publishers Weekly wrote that the book is an "extraordinary science fiction epic... perfect for fans of big ideas and intimate reflections.

"[8] A writer for Tor.com said "The Vanished Birds may be one of the best debuts of 2020" and praised the way in which the plot developed and showcased the interconnected lives of the characters.