ALTERNATE VERSIONS
In one possible future dubbed Here Comes Tomorrow, which now no longer exists due to the Phoenix Force, the Earth was ruled by the ancient and malevolent self-aware bacteria called Sublime. Inhabiting the body of Hank McCoy - the Beast - Sublime used his army of genetic
creations, called Crawlers, to cleanse the world of what he called unclean. Still acting in their capacity of outlaw heroes, the X-Men were the only existing force capable to opposing the Beast. Leader of this group of mutants and also headmistress of the Xavier Institute was Xavier’s sister, Cassandra Nova.
One hundred fifty years had passed since the destruction of the school by the faux Magneto, and slightly longer since Cassandra had laid waste to the nation of Genosha. Now a century and a half later, Cassandra was the torchbearer for Xavier’s school and his X-Men. It is unclear how this intervening time had changed both Cassandra’s mentality or the X-Men’s outlook on her, however it is clear that she now cared about what she had previously tried to destroy.
One could surmise that Emma’s plan had worked, and that the synthetic brain of Stuff had successfully rehabilitated Cassandra and convinced her of the nature of reality and her place in it. 
However, the mystery remained of how Cassandra escaped her cell… until a critical piece of information was gleaned from a conversation between Cassandra and her ever-present friend, Martha Johansson.
Clearly Cassandra still inhabited the body of Stuff - the reference to her “synthetic alien body” leaving no mistake. However, Martha’s unspoken wish to call Cassandra by another name - Ernst - evidently one of endearment that she had used in the past provided an essential piece of the puzzle, from which one may extrapolate the rest. In this reality the pre-teen girl in Xorn’s special class, Ernst, had in fact been Cassandra Nova.
When Bishop was trapped far in a potential future, he became embroiled in a war against an evil force known as the Revenants (also known as Mummudrai), led by the Revenant Queen. Using a revenant, the Demon Bear, she managed to hitch a ride using Bishop back to the present day.
She managed to possess a young, psychic mutant named Ginny, and utilize her power to start a cult known as the White Robes in Los Angeles. She used the cult as a way to gather power and summon more revenants from the dark parts of her followers before putting her ultimate plan into action. She wanted to pull down the veil between the material world and the underworld in an event known as the Great Corruption, which would lead to the destruction of all living things. This was the event that Bishop had fought to stop in the future and now Cassandra was going to trigger it 1,000 years early.
The only heroes on hand in L.A. that could respond to this threat was the X-Force team led by Psylocke that had rescued Bishop from the Demon Bear corruption when he first returned from the future. The team interrupted Nova, now called the Owl Queen, during her ritual and began fighting the army of revenants. Psylocke was even captured and the Owl Queen used her power to summon her evil Revenant. The Owl Queen offered Psylocke the chance to take over the body 
of this Revenant, which was in the form of her original body, but Psylocke refused the temptation and broke free. The team managed to fight back to the point that they were able to free Ginny from the possession of Cassandra but she instead took possession of the Psylocke Revenant. The actual Psylocke grabbed her from behind and used her psychic dagger to trap Nova in the physical body of the Revenant before stabbing and killing her former body, ending the Great Corruption ritual just in time. Cassandra was dragged back beyond the veil to the underworld, her plan having failed.
The future reality known as X-Men: The End saw Cassandra Nova in possession of Lilandra’s body and thus the Shi’ar Empire once again. Her superseding goal, as always, was to torture her brother Charles. Thus, she dropped the facade and psychically attacked the man when he unwittingly came to his former lover for help in the X-Men’s darkest period. She sent a mind-controlled imperial Superguardian back through a wormhole to Earth in an attempt to destroy the planet and trapped Xavier’s mind in the Superguardian Stuff, exactly as had been done to her so long ago. As a final act of vengeance, she killed Lilandra in front of Charles and left him with the blame for her murder. This led to a brawl between the Superguardians and the X-Men, giving Cassandra enough time to possess Xavier’s body. When everybody was finally made
aware that Nova was the true enemy, all groups converged to stop her. Cyclops decapitated Xavier with his optic blast but the combined psychic energies of Xavier and Cassandra allowed her to exist in a non-corporeal state. Cassandra’s threat was finally ended when Jean Grey hatched from a Phoenix egg and combined her powers with Cable in order to dissipate the energies of Nova. With everyone believing that the villain was vanquished, a Nova-possessed Rachel Grey blasted a hole through her mother from behind, claiming the Phoenix for herself. The Phoenix-empowered Cassandra started slaughtering the X-Men and Superguardians, and even caused the Shi’ar sun to go supernova. However, a combination of Jean and several other X-Men formed a Tree of Life with the intent to transcend this plane of existence. The final piece of the Tree needed was for Cassandra and Charles to both admit their wrong-doing and work together. They argued at first that they could not but finally agreed to try, ascending with the rest of the X-Men through the power of the Phoenix.
In the Battleworld domain of Mutopia, the events of E is for Extinction led to Charles Xavier blowing his head off with a pair of guns, rather than let Cassandra possess his body. What really happened after his death was that, while Jean Grey was mind-linked with Xavier at this moment, 
both Xavier siblings transferred their consciousness over to Jean’s, who promptly went into a coma and encased herself in a Phoenix egg. Charles and Cassandra battled for dominance within Jean’s mind for years until Charles left Jean’s mind to help the X-Men by possessing a recently deceased Quentin Quire. This allowed Cassandra to take over Jean’s mind and emerge from the egg with the powers of the Phoenix. The threat was only ended when Xavier possessed Wolverine’s body and distracted Cassandra on the astral plane, while Logan kissed Jean to wake her up. The two were forced to kill each other in order to fully end Cassandra’s terror.
In What If... Ord Resurrected Jean Grey Instead of Colossus? Cassandra Nova put her plan to release herself from the X-Men’s containment unit into motion more quickly. With Emma emotionally reeling from the return of Jean Grey early into her relationship with Cyclops, she was more vulnerable
than ever to Nova’s manipulation. Cassandra convinced Emma to take on the power of the Phoenix, sealed within the hearts of her Stepford Cuckoos, before Jean had the chance. Thus, Cassandra could be freed with the power of the Phoenix. However, the combination of Emma’s subconscious rebelling, Jean revealing Cassandra’s presence, and Kitty Pryde literally ripping out a Phoenix empowered Emma’s heart, led to both Emma and Kitty’s deaths. Unknown to the X-Men, Cassandra had survived by possessing the sentient Danger Room.
In the Battleworld domain structured after the X-Men ‘92 animated series, the X-Men traveled to Clear Mountain, where violent mutants were sent to change their ways and seek a new path. Upon arriving, the director of the facility, Cassandra Nova, greeted them and offered them a tour, demonstrating how many formerly violent mutants were now acting peacefully. A dubious Charles 
Xavier used Cerebro to investigate Clear Mountain and found an antagonistic Cassandra Nova ready to do battle on the Astral Plane. A flashback revealed that the Shadow King had found a cloned body of Xavier and merged with it to become the Shadow Queen. Back in the material world, Cassandra captured and began brainwashing the X-Men, successfully turning Wolverine, Gambit and Rogue. However, while trying to turn Jean Grey, Psylocke of X-Force showed up to stop her by shoving her psychic knife through Cassandra’s head. Regardless, Nova’s plan to assassinate Baron Robert Kelly, leader of the domain, using a giant Sentinel was already in motion and her team of Wolverine, Gambit and Rogue attacked X-Force. In pursuit of Kelly, Cassandra and her pawns were taken out by the other X-Men and X-Force. Xavier returned and managed to drive the Shadow King out of Cassandra with the help of the other psychic mutants, allowing the freed Cassandra Nova to disappear in the confusion.