Born at the same time as the X-Men's leader, Charles Xavier, Cassandra's psychic form didn't have a host. She thus copied her "brother's" one, although that would later make her go bald. Her brother had psychically destroyed her once he sensed that she had some "unsane" thoughts, but she hid in sewers and plotted and waited to form herself another body.
Cassandra Nova was created by Grant Morrison and Frank Quitely
It has later been established by telekinetic telepath Jean Grey, host of the Phoenix Force, that Cassandra Nova is a Mummundrai, based on an ancient Shi'ar s legends. Mummundrai are the opposites of the originals, and Jean says that everyone has to meet their Mummundrai in the womb. It is the first contact a human ever has with alien lifeform. Cassandra managed to obtain her body because of the power of Charles' Psyche.
After the Mummundrai (Cassandra) absorbed Stuff, Morrison did not elaborate what the X-Men did with the possessive creature. In Chuck Austen's New X-Men, Cyclops and Beast investigate Mummundrai's containment unit following the destruction of the mansion, only to never find it (and seeming not to care once they don't). In Joss Whedon Astonishing X-Men we get a glimpse at the Mummundrai's containment device and discover that Professor Xavier had it built so that no one could breach it's security. But, do to some mind tampering by a possessed Emma Frost, Kitty Pryde manages to phase it out of it's Containment shell. It was hinted in Morrison's run that Cassandra Nova took on the form of Ernst once she was placed inside the body of Stuff as part of her reprogramming. The final hint was in Here Comes Tomorrow (New X-Men #153), where she tells Martha Johansson, who Ernst was always seen around, that "of course you can still call me Ernst."
Major Story Arcs
The Genocide at Genosha
Once her body was rebuilt, Cassandra plotted revenge against her twin brother. She persuaded Donald Trask III (last living relative of Bolivar Trask, inventor of the sentinels) that he should activate a pair of sentinels and send them on the island of Genosha, home to many mutants. 16 million mutants were counted as dead, but Charles Xavier, Emma Frost and Lorna Dane (also known as Polaris, daughter of the master of magnetism: Magneto) survived the massacre. Cassandra then copied Trask's DNA to have access to the Sentinel's "Minds", and give them orders, since only one with Trask DNA can control them. When Cyclops and Wolverine found Cassandra, she has already infected her body with millions of pieces of nano-technology.
They brought her to the X-Mansion, but she managed to free herself, and defeated nearly all the X-Men... just like that. She then accesses Cerebra (an evolved version of the original Cerebro) and implants her mind in Xavier's body and his in her's. Emma Frost arrives at that moment and snapped her neck (she still holds a grudge for Cassandra murdering all her students while she was teaching back in Genosha), and actually killing not Cassandra, but Charles. Xavier, still alive but weak, couldn't warn the X-Men about the body-switch in time: his twisted sister shot him as fast as she could.
Cassandra (using Charles' body) telepathically makes a student of the Xavier Institute, known as Beak, to beat up Henry Mc Coy as he discovered that Xavier and Cassandra shared the same chromosomal structure. Then, Cassandra contacted the Shi'ar (race led by Empress Lilandra, Charles' long-time lover). Driving Lilandra insane, Cassandra manipulates her into destroying the Empire, using the Imperial Fleet. Lilandra is then manipulated into sending the Imperial Guard to remove from the core of Earth absolutely any mutant population, including the X-Men. The X-Men fight the Guards, before convincing them of the truth.
Finding out about Cassandra's threat-level, the Guard, realizing she betrayed them, fight with her, but she defeated them and went to the X-Mansion. She plots to use Cerebra, and destroy all mutants via it, but Jean Grey(already possessed by the Phoenix Force, which augmented her power) was there before and put a piece of Xavier's consciousness in every living mutant Cerebra could locate. Focusing on all mutants, thanks to Cerebra, Xavier's mind was brought back together. Meanwhile, Jean attacked Cassandra on the psychic plane, forcing the Mummundrai to exit Xavier's body. Cassandra was then only a psychic entity, handicapped by the absence of a body. She freaks out, since she is thus blind, and cannot see anything. Emma Frost arrives and concludes a deal with the witch: she will give her back her flesh in exchange of a guarantee she and the Stepford Cuckoos would survive. It was in fact a trick, being that the body was an alien shape-shifter known as "Stuff", where Cassandra's essence was forever stuck.
During the John Cassaday/ Joss Whedon run in 'Astonishing X-Men' 's " Torn", Cassandra returns, scheming revenge on the X-Men. With Sebastian Shaw, Emma Frost, Perfection and Negasonic Teenage Warhead, they form a new age for the Hellfire Club... that doesn't last that long. They appeared near the end of " Dangerous", where Cassandra implies that she is the one who triggered Emma Frost's secondary mutation (the ability to turn into a diamond) which saved her from the massacre. Emma promised in exchange she would infiltrate the X-Men for her unconciously, since Cassandra erased her memories about their conversation.
When Emma tricked Cassandra to enter "Stuff", Cassandra managed to implant a piece of her mind in Emma's, manipulating her with her guilt as being one of the only survivors of the Genoshan Massacre and the fact that she used to be the villain known as the White Queen of the old Hellfire Club. Emma thus projected images of Cassandra Nova, Sebastian Shaw and Negasonic Teenage Warhead, one of the many genoshan victims. (all in telepathic link). She also made a version of her a few years back, that she called " Perfection". They then attack the X-Men seperately, especially Nova: Cassandra reduces Beast to the primitive form of a... well, a beast and gives Wolverine a spark of youth by turning his consciousness into that of when he was 10 years old; Shaw attacked Colossus, while Emma took on Cyclops, removing his optic-beam power. Negasonic Teenage Warhead took care of stripping Kitty Pryde of all controls over her phasing abilities.
Making Kitty belive that she gave birth to a baby boy named Michael, who's father is Colossus, granted Emma Frost and Cassandra Nova the power to manipulate the intagible girl into retrieving Nova's body, trapped in "Stuff"'s form, for them. They then wanted Kitty to be Cassandra Nova's new host body permenantly, although that plan was foiled since A: Cyclops arrived saving the day, and B: Kitty's mind became too strong to breach. It is then said that Emma's plan all-along was to murder Kitty to ensure that Cassandra wouldn't move her spirit to another body. Nova then believes that Armor (or Hisako Ichiki) is a more likely host, being less mind-strong then the "Pryde girl". In Emma's mind, Cassandra is influencing her to put her consciounsness into Hisako while in the real world, Cyclops tries to convince Emma to shut Cassandra back into "Stuff", for good this time. Cassandra then disappears in " New X-Men: #156", but the X-Men managed to prevent her to possess Armor. Blindfold decrees at the end of that story that, thought the X-Men were brought to space, they would not all come back to Earth after...
Powers & Abilities
Cassandra Nova is one of the mummudrai. They are incorporeal parasites, composed solely of emotional energy born from the astral plane of existence. The mummudrai are usually forced to fight with the mind of their host over a body. However, given the vast potential in Xavier's genome, Cassandra Nova was able to build her own body, mimicking human traits as best she can. Cassandra Nova has access the full spectrum of mutant functions in Xavier's genome (meaning she has the powers of Charles Xavier, the ones he could have and the ones he might receive as a result of latent mutation), granting herself vast psionic powers . These powers include telepathy, telekinesis and a phasing ability. She was able to block the considerable telepathic abilities of Charles Xavier, create psionic armor, forge battle armor from the materials around her, disintegrate the complete tissue of Wolverine's arm and make her body completely intangible to an extent that even allowed her to withstand a direct blast from Cyclops.
She has all the powers of the "average" mummudrai as well, which are astral projection and mental possession. Her telepathic capabilities are so advanced that she was able to hide her possession of Charles Xavier's body over quite some time despite directly interacting with considerable telepaths like Jean Grey, Emma Frost and the Stepford Cuckoos at the same time. The mummudrai are able to copy the DNA of sentient beings and use it to construct physical bodies for themselves. The mummudrai can also manipulate the DNA it copies to act as a rapid healing factor or to phase through solid matter. Further, they can manipulate the DNA of others, breaking it down at the molecular level. First using her DNA copying ability, she mimicked Donald Trask III, a relative of Bolivar Trask, so that she can voice command the Sentinels, who obey the Trask family line, to attack Genosha. She said it took her ten hours to read and copy the three billion base letters of Donald's DNA sequence. Then she manipulated Emma Frost's DNA to express her secondary mutation.
Earth-15104: Here Comes Tomorrow
In the Here Comes Tomorrow future timeline, Cassandra's reeducation was a complete success; she had embraced Xavier's dream and went on to become Headmistress of the Xavier Institute. Instead of simply going by the name of Cassandra Nova, she added the Xavier surname to her own, now calling herself Cassandra Nova Xavier. Alongside Wolverine, the three remaining Stepford Cuckoos (now calling themselves the Three-in-One), Beak's grandson Tito Jr, E.V.A. and No-Girl ( Martha Johansson), Cassandra became one of the X-Men, fighting against Sublime and its armies of Crawlers, led by Apollyon. Cassandra was destroyed by Sublime after it unleashed Phoenix on the X-Men. However, this time-line diverged from Earth-616 when Jean Grey reached back and psychically forced Cyclops to accept Emma's offer to run the Xavier Institute together. In the current time-line, Cassandra remembered her original identity.
X-Men: The End
Cassandra factors prominently in the future depicted in X-Men: The End storyline (Book 3). In this timeline she remains a villain. She is primarily responsible for the Shi'ar attacks on the X-Men, which she had manipulated in the hopes of gaining control of Jean Grey and the Phoenix Force. Her hope was to bond with the Phoenix and thus be able to destroy all existence. Though she was successful, Jean and Psylocke are able to subdue Cassandra. Jean then tells Cassandra that they are all going to transcend reality. Jean uses her connection to the Phoenix to bring a host of X-Men together (both dead and living) so that they can all become one with the universe while bringing others back to Earth. Xavier and Cassandra admit that they are scared of each other, and Jean tells them that this is part of being human. Then, she and the resurrected X-Men form a giant Phoenix and become part of the universe itself.