The year is 2049 and Christine Pizan is living aboard a space station called CIEL that is run by a dictatorial leader named Jean de Men. Christine is turning 49 years old. She will be put to death on her 50th birthday, as resources are scarce and citizens of CIEL are not permitted to live into old age. The earth below has suffered a series of cataclysmic events leaving it largely uninhabitable. Christine and her best friend Trinculo are imprisoned for breaking Jean de Men's draconian rules, and she learns that Trinculo will be executed for his involvement with a resistance force on Earth fighting against de Men.

The resistance is led by Joan, a young woman with a special connection to the earth. Joan has superhuman powers that were first revealed to her in childhood, heralded by a magical song and a blue light shining from her forehead. As a resistance fighter, she battled Jean de Men's military forces, along with her brother Peter and her close companion Leone. After having a premonition about the further destruction the war could cause, Joan triggered a major cataclysm on Earth by lying down in the dirt and summoning her powers. This caused de Men and his followers to retreat to CIEL, where they have lived ever since.

On CIEL, Christine meets a woman named Nyx, who explains that she and Joan are both engenderines, meaning they have special powers that allow them to move and affect matter in unique ways. Christine hatches a plan involving Nyx to save Trinculo and kill Jean de Men during a theatrical production which she will direct.

Meanwhile, Joan and Leone are living on Earth in Vietnam's Son Doong Cave. Earth is largely barren of life, and Joan's recalls a peculiar instance in which she and Leone happened upon a young boy, whom they called Miles. Miles had insisted there were other survivors, living hidden away, and that he must return to tell them that Joan was alive. She gave him a lock of her hair and a letter and sent him on his way.

Returning from a salvage mission, Leone is confronted at the door of the cave by a man. She stabs him before realizing it is Peter, Joan's brother. He had been living underground with the rest of the resistance and had received Joan's letter from Miles. Peter dies, but Joan uses her powers to resurrect him briefly. He tells her everything he knows, including how to get to CIEL, and then he dies again. The cave begins shaking wildly and then collapses. When Joan emerges from the debris, Leone is gone, kidnapped by Jean de Men's forces, and Nyx is there.

Nyx takes Joan to the dry riverbed of the Seine in Paris, where the resistance forces are hiding out. She explains that Joan can summon the powers of other engenderines and use her body to regenerate the earth, though she will die in the process.

Christine's play begins on CIEL. Jean de Men is present and holding Leone hostage. De Men cuts Leone open, removes her uterus, and eats it. Christine says the code word, “Joan,” and her actors attack de Men [244]. Under de Men's clothing, Christine observes the evidence of botched surgical procedures, a crude attempt at gender reassignment surgery. De Men was once a woman. Joan appears on the scene, along with an army of engenderine children who finish killing de Men. She rescues Leone and they flee.

Christine and Trinculo change the course of CIEL to fly into the sun, sacrificing their lives to destroy the vessel. Leone helps Joan to sacrifice herself and usher in the earth's rebirth, by once again lying down in the dirt.