Turning the tables
Assistance arrived in the form of the returning Cyclops and his new recruit, Xorn. Using his purported power of healing, Xorn managed to heal the X-Men, informing them that the sentinels in their bloodstream were now dead. Now returned to a semblance of their former health, the X-Men prepared for Cassandra.
As before, Cassandra made short work of the X-Men, easily bypassing Wolverine and the Beast, even going so far as to control the minds of the school’s students, having them attack in her place. Making her ways to the bowels of the Institute, Cassandra reentered the Cerebra chamber, intent on using the machine to attack the minds of every remaining mutant on the planet. She had not foreseen, however, how Jean had outmaneuvered her.
Before her departure, Cassandra had infected her previous body - the one in which she left Xavier - with the microscopic Sentinels that had ravaged it. Knowing that she had anticipated them trying to save the body in which Xavier’s mind now inhabited, Jean had done the opposite, allowing it to die. 
In an attempt to save Xavier’s consciousness and self, Jean had made room in her own mind and stored them within herself. Upon being cured by Xorn, Jean had used the Cerebra chamber to distribute those memories among all the mutants in the world - the same mutants Cassandra now touched via Cerebra. Finding Charles’ consciousness awaiting her, Cassandra’s own self was expelled from Xavier’s body, leaving her once again formless and hostless living emotional energy.
Vulnerable for the first time, Cassandra desperately needed a new host - which Emma Frost was apparently able and willing to trade. In exchange for the safety of herself and her prize pupils, Emma offered the previous body Cassandra had inhabited - that of Xavier’s “sister.” Scanning the DNA of the body and confirming that it was alive and the real deal, Cassandra accepted, inhabiting the body immediately.
Quickly, however, Cassandra realized that something was amiss. The body was not hers, but was in fact the 
Superguardian called Stuff, a shapeshifting artificial life form, which Emma had programmed to emulate Cassandra’s DNA. Now trapped within the synthetic brain, Cassandra found herself unable to think clearly, as well as being a student within a virtual reality classroom. Her new teachers were a programmed version Charles Xavier and Jean Grey-Summers, which intended to teach Cassandra anew.
Interlude
While Cassandra Nova had been decisively neutralized, the X-Men were cautious and locked her away in a cell in a lower level of the Institute. Now, with the crisis passed, the X-Men began to pick up the pieces, rededicating themselves to their cause of mutant rights and equality. Cassandra Nova had intended to destroy the X-Men by revealing their public identities. Now returned to his own body, Xavier realized that this was an opportunity - a real chance at the world of which he had only dreamed. The first step in this procedure was the rededication of the school.
As he had earned his place with the X-Men during the conflict with Cassandra, the enigmatic Xorn was given his own class of “special” students. The students consisted of mainly misfits and teens with social issues. The initial group consisted of Basilisk, Angel, Beak, Dummy, the brain of Martha Johansson… and an odd little girl named Ernst, who seemed to be a pre-teen with an aged and haggard-looking face.
In time, the X-Men would learn that Xorn was not who he appeared to be. In truth, he was Magneto - or at least someone purporting to be the X-Men’s oldest foe - who was attempting to break the X-Men from within. Using his relationship with these most rejected of mutants, Xorn built a new Brotherhood and eventually laid waste to both the Xavier Institute and much of the isle of Manhattan. Nevertheless, the X-Men prevailed and the threat of “Magneto” was eliminated - though not without the lives of several students, thousands of New York humans and even Jean being lost. [New X-Men (1st series) #150]
Afterward, while sifting through the rubble that was once the Institute, Cyclops and the Beast realized that the forcefield cell which had contained Cassandra could have been damaged in the attack. Though they searched, the body of Cassandra Nova was nowhere to be found. [X-Men (2nd series) #155]
Had Cassandra escaped? Had she been freed as a result of the mansion’s destruction? Or had someone released her from either her mental or physical prison? The answer, it seemed, lay not in the remains of the school Scott Summers and Hank McCoy had grown up in - but in a horrific possible future.
Here Comes Tomorrow
In one possible future, which now no longer exists thanks 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. [New X-Men (1st series) #151]
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. The pre-teen girl in Xorn’s special class, Ernst, had in fact been Cassandra Nova. [New X-Men (1st series) #153]