Aftermath: the forging of a retcon
The individual who had been the X-Man known as Xorn - and had then revealed himself to be Magneto (or supposedly so) was killed in New X-Men (1st series) #150. Grant Morrison, who had written this story, left the title in #154. It was almost immediately after this that Marvel editorial decided not only to undo the finality of Magneto’s demise, but two separate aspects of a retcon in two different titles: X-Men (2nd series) [renamed back from New X-Men] - now written by Chuck Austen - and the new Excalibur (2nd series) - written by Chris Claremont.
As stated before, the new Excalibur series [not to be confused with the later “New Excalibur” series] was set in Genosha, now a desolate, barren shell of its former glory. It was there that Professor Xavier intended to spend his sabbatical, helping to rebuild with survivors, as well as others who had come to the island for the same reason. After just a short while there, he ran into Magneto, still very much alive.
Xavier seemed hardly surprised at this, and almost nonchalantly informed him that the body he had carried to Genosha was of a mutant who had claimed to be Magneto. The unknown mutant had claimed that his “secondary mutation” was the ability to come back from the dead. Magneto himself, it seemed, had not only survived the attack on the island but had been completely unaware of the actions of his doppelganger in New York. He was likewise shocked when informed that the imposter had killed Jean Grey. After a brief conversation, where Xavier wondered if Magneto might have had any connection with the mutant in question, the subject was dropped - and was never mentioned again. [Excalibur (2nd series) #1-2]
Meanwhile, a much more convoluted version of the retcon began the same month as Excalibur (2nd series) #1, over in the newly renamed X-Men (2nd series) #157. 
After having just repaired the Xavier Institute and having reassigned the X-Men to new squads, Emma Frost detected the presence of a new and very powerful mutant in China. Likewise, Polaris herself was physically assaulted by a tear in the Earth’s magnetic field. Racing into action, Havok’s newly-formed squad of X-Men flew by X-plane to a remote area of China. There, they discovered a giant crater, which had replaced what was once a monastery. At the bottom of the debris, they found a young man, who had a helmet just like Xorn’s.
While Wolverine’s senses told them that this was not the same “Xorn” that they had previously encountered, the evidence of the area told them that person seemed to have a power similar to what they believed Xorn had possessed. In fact, Lorna continued to sense gravimetric and magnetic distortions around his head. Further, it seemed that this mutant had lost control of his powers, and that the whole area - if not planet - had not been consumed only because the containment helmet had been placed over his head by a man who had clearly given his life to do so.
After a brief run-in with the Chinese super-team called the Eight Immortals, this “new” Xorn was brought back to the Xavier Institute, where he was examined and questioned. There, it was determined that this Xorn’s true name was Shen Xorn - 
and that he was the twin brother of the other Xorn, whose true name was Kuan-Yin Xorn. It was further believed (at least by Emma) that Magneto had somehow “appropriated” the body of Kuan-Yin Xorn and had run amok. It was Kuan-Yin Xorn who had died - not Magneto.
As for the differences between himself and his “brother,” Shen Xorn was not a healer, but indeed was telepathic. Emma also believed that he possessed other abilities, though they would only learn of these in time. One thing she was confident about, however, was that Shen Xorn had nothing to do with Magneto. “Not now. Not ever.”
When eventually questioned by Havok, however, Shen Xorn informed he and Emma that the actions of his brother had not been caused by Magneto, but by someone else. He did not have a name of the individual, by Shen Xorn could tell that the person was fiercely hateful and malevolent, and had been hiding among them for sometime. Even then, the person sought to turn others against the X-Men. Their only intent was to destroy everything Xavier had built. When finished, Shen Xorn then promised Havok that he would help in any way that he could.
Nevertheless, Shen Xorn did not get the chance. Shortly thereafter, the X-Men were once again attacked, this time by a new Brotherhood of Mutants, led by Exodus. Seeing at least one innocent life taken during the battle, that of Sammy “Squidboy” Luc Pare, Shen Xorn decided that he could allow no more. 
Of his own volition, and encouraged by the battle-weary X-Men, Shen Xorn opened the containment helmet, exposing that black hole that was his mind. The remaining Brotherhood, along with the Juggernaut, were sucked into the void created by Shen Xorn, disappearing to parts unknown (later learned to be the Mojoverse).
Emotionally affected by the action, Shen Xorn decided that he needed time alone, away from the X-Men, in order to meditate on the immensity of his actions. Given his blessing by Havok, Shen Xorn departed. [X-Men (2nd series) #164]
Though he himself has not been heard from again, it has been revealed that Shen Xorn lost his powers during M-Day. [New Avengers #18] As he no longer possessed a skull or physical brain, it is unclear if he survived the transformation from mutant to human.
Kuan-Yin Xorn’s return?
A few months after Shen Xorn’s departure, a convoluted series of events occurred to bring back, albeit temporarily, the person once known as Kuan-Yin Xorn.
Many months previously, perhaps years, the Scarlet Witch had been growing slowly insane. Her madness culminated in the destruction of the Avengers as a group and several members specifically. [Avengers Disassembled] Realizing that she was the cause, the Avengers and X-Men traveled to Genosha, where the Witch had been hidden by her father, the still very much alive Magneto.
Realizing that the Avengers and X-Men meant her harm, Quicksilver whispered in his sister’s ear and her power ran amok, re-creating reality into a mutant utopian world, run by Magneto and his House of M. When the heroes of this re-created world realized that reality had been altered, they once again sought out the Witch, who remade reality as it was - with one difference: the number of mutants in the world was diminished from millions to hundreds. [House of M #1-8]
Unfortunately, the energies previously wielded by these former mutants was not extinguished, and they coalesced into a field of energy, which orbited the Earth. Eventually achieving a level of consciousness, the energy chose one of the few remaining mutants, an Alaskan postal worker named Michael Pointer, as a host. After a deadly conflict with Alpha Flight and a nearly-deadly battle with the Avengers, the Collective, as the Avengers began to call it, made its way to Genosha, where it met up with Magneto, now depowered and living alone in the ruins.
The Collective explained to Magneto that he was the only one the remaining mutants would rise up and follow. The Collective had previously tried this itself and failed - under the face and name of Magneto. When this confused Magneto, prompting him to ask who the Collective was, the Collective replied that he already knew - it was Xorn.
Apparently, after the destruction of Genosha at the hands of Cassandra Nova’s sentinels - and as Magneto remained convalescing on Genosha - the original and very much real Kuan-Yin Xorn had embarked on a plan just before or just after being recruited by the X-Men. [New X-Men Annual 2001, New X-Men (1st series) #122-126] Wishing to bring mutants together, Kuan-Yin had decided that the best way to do this was to attempt to do so under the guise of Magneto. After revealing himself as such, Kuan-Yin Xorn had attempted to do as he believed Magneto would have wished. Of course, he was ultimately stopped by the X-Men and killed by Wolverine. [New X-Men (1st series) #150]
It should be noted, however, that sequence of events does not take into account the words of Shen Xorn, who stated that the actions of Kuan-Yin Xorn were not his own, but coerced by an unseen and malevolent entity, who wished harm on everything Xavier had ever created. The two theories are not actually mutually exclusive, as Kuan-Yin Xorn did not seem to have any suspicious motives prior to his killing of the U-Men on the Institute grounds. At any point prior to that, Kuan-Yin Xorn could have been earnest in his wish to help the X-Men and their cause.
This new attempt at Xorn to empower Magneto’s dream - and in this case Magneto itself - failed as well. After having abandoned Michael Pointer’s body as host and attempting to graft itself onto Magneto, the Xorn-driven Collective was ultimately rejected by Magneto. Now without a host, the Collective was encapsulated by a force field, created by Iron Man, and then hurled into the sun by the Sentry. There, the collective of mutant energies seemed to dissolve and disperse.