Humans have left their home planet, Terra, and spread across the galaxy. During this wave of colonization, they encountered many different sentient alien species and eventually joined the Galactic Federation. Due to the Terranauts' rapid procreation, they became one of the two most powerful races in the Federation.

The other influential race came from a six-planet system known as Hexa. Long ago, every single planet in the Hexa system had been inhabited by an advanced race known as the Ancient Ra-Phael. These angelic beings had sophisticated technology, including sentient computers and teleportation centers that connected all six planets, honed physical strength and speed, and powerful psychic abilities. Then, suddenly, the Ancient Ra-Phael vanished.

Over a century before Kill the Crows begins, two races inhabited the Hexa system. The warlike Firaru--known to the humans as Hexanauts--made their home on the second planet of the system. These Hexanauts, both males and females, are physically imposing, with red eyes and hair of various shades of yellow. The fourth planet was inhabited by a telepathic race called the Ra-Phael, believed to be the descendents of the Ancient Ra-Phael. Hexanauts and Ra-Phael cannot interbreed, though humans can breed with either race.

The modern Ra-Phael had incredible physical beauty, a love of peace, and strong empathic talents that suited them for being superb diplomats. They were ruled by a queen and, on their home planet, dwelled amid a net of telepathy and empathy that linked all of their minds. This mental net was so spiritually satisfying that many Ra-Phael began forgetting to interact with others...or even eat to keep themselves alive. The members of the royal family had such strong telepathy that they could control the minds of other people as well as computers.

However, the pacifistic Ra-Phael had a dark secret. Occasionally a black-haired child with the capacity and talents for physcial combat was born. When such a child was born in the regular population, it was handed over to a clan of Black Ra-Phael who acted as bodyguards and assassins for the royal family. It was said that no Black Ra-Phael were ever born into the royal family itself...but this was because any such child was immediately killed. Finally, however, the last Ra-Phael queen could no longer bear to murder her children. After giving birth to a number of daughters who were acceptable as heirs, she stopped having her black-haired children killed, letting them grow up in the palace. She had two: a daughter named Euphemia, and her youngest child, a son named Mariliard. These two children suffered a life of complete ostracism.

One day, Euphemia entered into a forbidden romance with her uncle Navalfore, the queen's younger brother. He tried to take her off-planet, where they could live together safely, but he was unable to accomplish his goal and wound up being exiled. He eventually went to live on the education planet Naaka. There he married and had a daughter whom he named after his lost love. He also met up with Professor Oscarstein, the head of the planet, and his wife, a brilliant geneticist. Professor Oscarstein's wife created a son for them, named Olivie, using her genetic recombination skills. How she did so is unknown, but it is later speculated that she used DNA from herself, Navalfore, and a Hexanaut donor, combining all three races into one. Olivie grows up to have the striking beauty and strong telepathy of the Ra-Phael royal family as well as the enhanced physical strength and speed generally associated with the Hexanauts. Olivie joins the Galactic Federation's Military Intelligence.

About 80 years before Kill the Crows, the Ra-Phael homeworld is suddenly stricken by a fast-acting, incredibly deadly disease. The Federation sends a military fleet to quarantine the planet. The human commander of the fleet, deciding that it is too dangerous to risk the disease spreading, bombards the world with planetary crust-shattering missiles, killing nearly everyone. It is not discovered until afterward that the disease affects no one but Ra-Phael. The only survivor is the seven-year-old Prince Mariliard, who escapes the destruction by a desperate use of his powerful telepathic abilities. He is a throwback to the Ancient Ra-Phael, and his telepathy awakens the sentient computer left behind on the Ra-Phael homeworld. This computer saves his life and raises him until he is ready to go out into society and work on saving his race. Unfortunately, Mariliard had not escaped being contaminated by the disease, which will kill him if he uses his mental powers any further.

In the intervening years, the Hexanauts are furious that a planet in their system was destroyed by humans. The Third Galactic War develops between the Hexanauts and the Terranauts, among whom power is pretty evenly divided. The war lasts for ten years before ending in an uneasy truce.

Twenty years after the the Ra-Phael were massacred, Mariliard sets out on a mission to collect donated eggs and sperm from the Ra-Phael who survived the cataclysm by being offworld at the time. He receives permission from the Federation to start a new Ra-Phael homeworld on the fifth plaent of the Hexa system, Caiu. During the course of this mission, he is plagued by attacks from the secret society Ouroboros that is trying to prevent him from succeeding. He is assisted by Olivie, who is trying to rid the Federation of the pervasive Ouroboros threat. The two men become fast friends.

The prince speculates, based on Olivie's genetic background, that the Ancient Ra-Phael had genetically engineered their own race into the present-day Hexanauts in an attempt to use physical strength to compensate for and control their overwhelming mental powers. In order to prevent any combination between the telepathic Ra-Phael and the physically aggressive Hexanauts, they engineered their descendents so that any potential cross between the two would be lethal and produce no offspring. Then, some Ancient Ra-Phael remained behind on their homeworld, becoming the current Ra-Phael, while the rest set off into the galaxy and settled on Terra to evolve into humans. Notably, humans have a higher percentage of psychic abilities than the galactic average, and humans can interbreed with both Hexanauts and Ra-Phael.

Mariliard eventually succeeds in his mission, setting up his cousin Euphemia as the new queen of the Ra-Phael and freeing the last of the Black Ra-Phael from discrimination and their imposed status as assassins. It becomes apparent, however, that Ouroboros was originally founded by Navalfore, who used the secret society to research and develop the disease that killed the Ra-Phael in revenge for exiling him. Ouroboros overthrows the Hexanaut government and secedes from the Federation, intending to build a new government based on the principle of survival of the strongest. During the climactic struggle, both Olivie and Mariliard sacrifice their lives. However, the sentient computer of the Ancient Ra-Phael is able to bring their consciousnesses back in cloned bodies. The computer had suffered damage from the planetary bombardment, though, so it also creates a female clone of Mariliard, which the prince keeps secret from his best friend.

Roughly thirty years later, Mariliard again sacrifices his life--this time to save Olivie. The devastated officer is comforted by the female clone, named Freedom Zero (Frida for short). Olivie falls instantly in love with her, even though he isn't aware of her true identity. Despite the fact that Freedom considers herself male, since she has the same personality as Mariliard, Olivie forces a physical relationship upon her. The result is an unexpected child, a black-haired throwback to the Ancient Ra-Phael whom Freedom names Lucifard. In order to protect Frida and Lucifard from those who would seek a replacement for the well-loved Mariliard to be a symbolic leader of the Ra-Phael, Olivie officially acknowledges the boy as his son. That way the resemblance to the dead prince will not be remarked upon--Olivie himself, as Mariliard's "cousin," has a strong family resemblance.

Lucifard, a powerful telekinetic, follows in his father's footsteps and joins the military. There he meets up with a number of alien species. Most notable are the Hakushi, an influential long-lived race with orange eyes and white hair. The Hakushi are long-time rivals of the Ra-Phael, and they generally have cruel and sadistic personalities. Their race has the peculiarity that they stop maturing at different ages depending on the strength of their psychic powers. Those with weaker powers mature further, allowing them to reproduce, yet they have shorter lifespans. Those with stronger powers stop aging so early that their bodies have not matured enough to reproduce, though they live the longest. Olivie has a strong connection to--and dislike for--his Hakushi allies.

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