A Trojan Gambit
With Cassandra seemingly under their control, Cyclops and Wolverine brought her to the Xavier Institute, where the Beast studied her. Immediately, he recognized that while Cassandra looked human on the outside, nothing like her had existed before. He theorized that she was something new, neither human nor mutant - possibly a new species.
The Beast did not have time for greater examination, however, as Cassandra was not helpless. Having underestimated her abilities, the X-Men were not prepared as she burst free from the gravitational bottle, which had been meant to contain the Juggernaut. Making short work of the X-Men, Cassandra leisurely made her way to the Cerebra chamber. Though she knew that the machine would allow her to take hold of every mutant mind on Earth and extinguish it… she only wanted one.
Seemingly before she was able to accomplish her feat, Cassandra’s neck was snapped by Emma Frost. As the then-believed only survivor of the Genoshan holocaust, Emma had a particular score to settle with Cassandra. However, the X-Men at the time had no idea that Cassandra had succeeded with her latest gambit, using Cerebra to switch minds with Professor Xavier. As Xavier attempted to explain his predicament in the already mangled body of his sister, Cassandra - in Xavier’s body - used a pistol to end the apparent threat.
Having no clue as to the reality of what had just happened, the X-Men were equally unaware of the ulterior plan of Cassandra shooting her own body. Not only did she effectively incapacitate her brother, Charles, but by shedding the blood of her own body she had infected the X-Men with her blood, which she had infected at the Master Mold facility with Nano-Sentinels, microscopic machines which would eat at their immune system, weakening them.
While the X-Men reeled at Xavier’s actions, Cassandra continued to keep them off balance, almost immediately booking “Charles” on talk shows. On one such show, Cassandra announced to the world the X-Men’s greatest secret: Xavier and the X-Men’s true identities. [New X-Men (1st series) #116]
With their identities exposed, both prospective students and the watchful eyes of the world descended on the Xavier Institute. Protestors began to amass at the outside gates of the school. Inside, while the rest of the 
X-Men attempted to make sense of Xavier’s actions, the Beast continued his research on the comatose but still living body of Cassandra Nova. Making a shocking discovery on the genetic match between her and the Professor, the Beast confronted him.
The shocked Beast was ill equipped to handle the psychic attack from Cassandra, now being the most powerful telepath on the planet. Further, Cassandra used her abilities to control a recently enrolled student nicknamed the Beak, forcing him to use his titanium baseball bat to beat him. As the Beast lay on the floor, slipping into a coma, Cassandra wheeled Xavier’s body outside, where Lilandra, empress of the Shi’ar Empire, had come at his request. Eyeing the flagship of a galactic empire, Cassandra imagined what it could do in the wrong hands. Having told the X-Men that he wished to depart for a vacation with Lilandra, Cassandra departed the Earth, to now lay havoc among the stars. [New X-Men (1st series) #117]
Across the cosmos, Cassandra made the destruction of Genosha but a first step in her grand scheme of death and chaos. Clothed in the body of Xavier, Cassandra took control of Lilandra’s mind, having her order her generals to make war upon their own people. Across the Shi’ar Empire, the imperial battle fleet brought doom to their galactic civilization, though none dared question the empress - none except Lilandra’s loyal advisor, Imperial Sage Araki III. He alone seemed to recognize Xavier as being what he truly was, the anti-self of their ally - his Mummudrai. [New X-Men (1st series) #125]
Not all was going as planned, however, for Cassandra. The Shi’ar Superguardian named G-Type reported that contact had been lost with the Superguardians which had been sent to Earth to cleanse the remaining mutant population of the planet, starting with the X-Man. Further, the two X-Men which had been captured, Cyclops and the team’s newest group, the enigmatic Xorn, had escaped. Subsequently attacked by both mutants, as they had been held captive on the same ship, Cassandra decided to activate the ship’s self-destruct and return to the Institute, to finish the job herself.
Meanwhile, at the Institute, the X-Men had been using the intervening weeks to put together what had been transpiring under their noses. Trapped in the body of Cassandra Nova, Xavier had managed to reach out with his mind and animate the comatose Beast, finally able to communicate to his former students his predicament. A subsequent telepathic investigation into Xavier/Cassandra’s mind had revealed to the group Cassandra’s true nature and relationship to Charles. Then, after his recovery, the Beast had determined why they were all experiencing various colds and other ailments - the microscopic Nano-Sentinels, which were now attacking their white blood cells.
Though all sick, tired and semi-delirious, the X-Men had managed to fend back the first wave of Shi’ar Superguardians - knowing full well that Cassandra was returning herself for the final showdown. Refusing defeat, Jean hatched an idea. So far, everything had transpired according to Cassandra’s plan. She had thought it all through, every step of the way on a scale they could hardly imagine. The answer lay in doing something she would not expect of them.