Cassandra Nova began life at the same time as Charles Xavier. Conceived without a body; Cassandra improvised one by copying Xavier's DNA to make her own body, effectively becoming his twin sister. She grew with her brother until the time when Charles sensed her monstrous thoughts. Charles attempted to kill the creature, resulting in its physical body being stillborn. Despite this, 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. During this time, she grew convinced that the womb in which she had fought Charles and the universe she now inhabited were one and the same, a universe in which only Charles and her were real, and that her purpose was to destroy every illusion Charles held dear: his dream, his X-Men and his beloved Lilandra.
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 on the astral plane, 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, Cassandra'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.
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Genocide
After she was able to rebuild herself, Cassandra 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, programmed 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 Cassandra's neck (Emma had been in Genosha teaching during the attack and witnessed her students massacred). Trapped in Cassandra's broken body, Xavier was unable to warn the X-Men before Cassandra, now in Xavier's body, shot him.
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Imperial
Now in Xavier's body, Cassandra mentally forced the Xavier Institute student Beak to beat Beast into a coma after he discovered that Xavier and Cassandra shared the same DNA. Cassandra Nova then contacted the Shi'ar, whose leader was Majestrix Lilandra, Xavier's lover. Cassandra manipulated the Shi'ar Imperium, driving Lilandra insane using her to make the Shi'ar Imperial fleet destroy the empire. Cassandra 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 Cassandra's treachery and realizing the danger she posed, the Imperial Guard fought Cassandra, who defeated them and headed into the mansion. She had planned on using Cerebra to 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 Cassandra used Cerebra and focused on all the mutants, the pieces of Xavier's mind were brought back together and he was able to force Cassandra out of his body.
Without a body, Cassandra became pure psychic energy, bodiless and blind. Emma Frost tricked Cassandra into returning to what appeared to be her old body, which was in reality the alien polymorph "Stuff."
Cassandra's essence entered the body and was locked into a self-repeating program in the synthetic brain.
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Ernst
"Planet X" hinted and "Here Comes Tomorrow" directly implied that Cassandra had taken the form of the young mutant Ernst; however, in New X-Men #156 (written by the much criticized Chuck Austen), Cyclops and Beast investigate Cassandra's containment unit following the destruction of the mansion, only to find it empty. Whether these two characters knew about Ernst's connection to Cassandra is unknown.
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Hellfire
Cassandra Nova with Emma Frost. Art by John Cassaday.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, Cassandra'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.
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Powers
The mummudrai are usually forced to fight with the mind of their host over a body. However, given the vast potential in the Xavier's genome, Cassandra Nova was able to build her own body, mimicking human traits as best she could. Cassandra can also manipulate the DNA it has copied to act as a rapid healing factor or to phase through solid matter. After copying the DNA of Charles Xavier, the mummudrai Cassandra Nova accessed the full spectrum of latent mutant functions in his genome (this means she has the powers of Charles Xavier, the ones he could have had and the ones he might receive, as a result of latent mutation), granting itself vast psionic powers. These powers include: telepathy, telekinesis, and the ability to release an astral form, which she focuses both her telepathy and telekinesis. She has all the powers of the "average" mummudrai as well, which include the latter explanation.
Although it has never been specifically said, Cassandra Nova Xavier may be the mutant girl named Ernst. Ernst has not display any of the abilities Cassandra has, but only possessed superhuman strength. However, the fact that Cassandra inhabits the body of Stuff, the Shi'ar Superguardian, which can mimic not only the form but the DNA of any being, it is possible she is Ernst. And as such, Cassandra should be capable of regaining both her hard and soft psionic powers as well as becoming capable of shapeshifting. This also potentially protected her from the M-Day wave that depowered her "brother" Professor Xavier. Generally, the M-Day wave appeared to depower entire families, though there have been a few other exceptions.
She is also extremely intelligent, though Jean Grey (Phoenix) said she merely mimicked human knowledge and behavior.
