Two years after surviving an assassination attempt, seventeen-year-old Ella and her team of psychically-gifted agents navigate political turmoil and personal growth while maintaining their cover as wealthy teenagers, until the suicide of a friend leads them to encounter Asherina—a telepathic member of an ancient underground human species. Asherina reveals that her people have been hiding from surface dwellers for half a million years and warns of an impending solar catastrophe, proposing to combine their underground cities with the team's planned tunnels to save humanity from both an approaching war and a solar explosion that could destroy all surface life.
A human woman named Asherina from an ancient underground civilization meets with military Commander Beaker, revealing that her people have lived secretly beneath the surface for 600 years and are genetically similar to surface humans. Despite Beaker's skepticism and Asherina's refusal to reveal her city's location or allow official documentation, she joins a classified military project and moves in with team member Ella's family, bringing her husband and baby as they prepare for some urgent, undisclosed threat.
Ella writes a fictional story for her writing class about her future self at age 57, which includes helping a young woman named Chessa who crashes a stolen spacecraft and is revealed to be from an underground colony. After reading the story, Asherina (who appears to be Chessa's mother in real life) suggests the story might be prophetic and discusses the need for building more underground shelters for an unspecified future crisis.
Asherina and her unconventional crew have found success with their revolutionary shelter designs, though Ella struggles with the fact that only wealthy buyers can afford their life-saving technology while pushing for broader legislative changes to protect everyone. Their peaceful existence is shattered when armed attackers attempt to kill them at the Patel family home, forcing the girls to use their weapons and psychokinetic abilities in deadly self-defense before relocating to a secure compound.
Seventeen-year-old Eileen discovers two injured fairies in her backyard who become trapped in the human world after eating tainted cheese, and with help from a mysterious Navy Commander, she begins caring for them as they slowly transform into human-sized girls she considers her sisters. However, Eileen awakens to discover the entire fairy experience was a vivid shared dream experienced by multiple people in her village, leading her to rejoin a group investigating interdimensional rifts that may be connected to the prophetic visions.