Cassandra Nova began life the same instant Charles Xavier was conceiived. The only exception is she was conceived without a body, so she improvised. She took Xavier's DNA and copied it (literally spliting Charles unborn zygote) to make her own body, effectively becoming his twin sister. She then grew with her brother until the time when Charles sensed its monstrous thoughts, Charles attempted to kill the creature resulting in its physical body being stillborn. However, the creature survived as chaotic cellular matter and clung to a sewer wall for decades, rebuilding its physical form and perfecting its effort to mimic human traits.
Jean Grey later discovered that Cassandra Nova is the mummudrai (from a Shi'ar legend, meaning opposite) of Charles Xavier. "Legend says each of us faces our own personal mummudrai in the womb, shortly before birth - it is our first experience of the alien, the other, the different". In reality, the mummudrai are a parasitic species born bodiless as psychic energy (generally within the mind of the original), and it was only through becoming entangled with Charles Xavier's developing telepathic mind that Cassandra Nova created a body for herself.
Of comparable, if not greater, power to Xavier, Nova's entity somehow survived; clinging to a sewer wall and building up her strength, and in time building her own body from her brother's DNA.
After she was able to rebuild herself, Nova returned with a vengeance. She convinced the last living relative of Bolivar Trask, Donald Trask III, to activate a pair of enormous wild sentinels and send them to destroy the mutant homeland of Genosha, killing 16 million mutants. Cassandra duplicated Trask's DNA so she could also issue orders to the sentinels, programed to obey only those with the DNA of a Trask. Cassandra infected her own body with millions of nanosentinels just as she was captured by Cyclops and Wolverine.
Cassandra was taken to the X-Mansion, were she broke free and defeated most of the X-Men easily. Cassandra then put herself into Xavier's machine Cerebra (an enhanced version of Cerebro) and switched minds with her brother before Emma Frost snapped Nova's neck (Emma had been in Genosha teaching during the attack and witnessed her students massacred). Trapped in Nova's broken body, Xavier was unable to warn the X-Men before Nova, now in Xavier's body, shot him.
Now in Xavier's body, Cassandra made the Xavier Institute student Beak beat Beast into a coma after he discovered that Xavier and Nova shared the same DNA. Cassandra Nova then contacted the alien race the Shi'ar, whose leader was Majestrix Lilandra, Xavier's lover. Nova manipulated the Shi'ar Imperium, driving Lilandra insane using her to make the Shi'ar imperial fleet destroy the empire. Nova also made Lilandra send the Shi'ar Imperial Guard to wipe out the mutant population of Earth, starting with the X-Men. The Guard fought the X-Men until they were able to show the truth to the Imperial Guard.
Angered at Nova's treachery and realizing the danger she posed, the Imperial Guard fought Nova, who defeated them and headed into the mansion. She had planned on using Cerebra eliminate all mutants. However Jean Grey (who was becoming increasingly more powerful due to a manifestation of the Phoenix entity) was able to split Xavier's consciousness into pieces and store a little part of him in every single living mutant mind. When Nova used Cerebra and focused on all the mutants, the pieces of Xavier's mind were brought back together and he was able to force Nova out of his body.
Without a body, Nova became pure psychic energy, bodiless and blind. Emma Frost tricked Nova into returning to what appeared to be her old body, which was in reality the alien polymorph "Stuff."
Nova's essence entered the body and was locked into a self-repeating program in the synthetic brain.
"Planet X" hinted and "Here Comes Tomorrow" directly implied that Nova had taken the form of the young mutant Ernst. However in New X-Men #156 (written by the much criticed Chuck Austen), Cyclops and Beast investigate Cassandra's containment unit following the destruction of the mansion, only to find it empty.
Cassandra, back in her original form, returned in the "Danger" storyarc of Astonishing X-Men, alongside Sebastian Shaw of the Hellfire Club.
So far, it has been revealed that she used her vast psionic powers to awaken Emma Frost's "secondary mutation" which granted her the ability to turn herself into "living diamond" in exchange for the favor of Emma infiltrating the X-Men. Hints are also given that Emma in return did something more for Cassandra.
In the Here Comes Tomorrow future timeline, Nova's reeducation was a complete success; she had embraced Xavier's dream and was now Headmistress of the Institute. However, this timeline diverged from Earth-616 when Cyclops agreed Emma's offer to run the Xavier Institute together.
