Picking Up the Pieces
Trusting the instincts of Threnody, Nate contacted the Avengers. They agreed to help him investigate the matter of Onslaught, although they had doubts about Nate’s story, as his accusations all pointed towards a man they all trusted: Charles Xavier. When the Avengers and X-Man made it to the destroyed Xavier Institute, they were astonished and scared by the unpleasant view, especially as the Quinjet’s systems weren’t picking up any lifesigns. Nate Grey used his telepathic powers, though, and sensed that the X-Men were still alive, apparently still shielded by the mansion’s defensive systems. He also discovered that Xavier was no longer with them, leaving him very angry. Earth’s mightiest heroes decided to land and scout the area, but before they could, they were attacked by the X-Men.
Barely having survived Onslaught’s attack and still weary, the X-Men were suspicious about the Avengers, thinking that they might be another illusion created by the near omnipotent villain they had just fought. Naturally, the Avengers didn’t understand what was going on, and confusion turned to battle. Still aboard the Quinjet, Nate Grey was equally confused by spotting Jean Grey, who he recognized as his traveling companion Madelyne Pryor. Even more suspicious than before, he entered the minds of the X-Men to find out what was going on there. Making use of his formidable telepathy, he reconstructed an image of Onslaught from the collective minds of the X-Men for the Avengers to learn the reason for the X-Men’s behavior. They were even more shocked when Cyclops revealed that Nate’s accusation was correct - Onslaught was Charles Xavier, possibly manipulated by Magneto. With Jean Grey telepathically confirming the Avengers to be the real deal, everyone calmed down, and the gathered heroes went to what was left of the War Room to form battle strategies.
Revelations and Wargames
While the X-Men were making battle plans, Bishop found himself replaying the distress signal Jean sent, realizing that the message he saw in the future long ago referred to the recent battle he fought with Onslaught. In his timeline, Onslaught had killed the X-Men, and not Gambit, like Bishop suspected. Bishop apologized to the Cajun, and the two joined the other X-Men and Avengers in the War Room. The X-Men showed the Avengers simulations of Onslaught, Xavier and Magneto. Going by the color scheme of Onslaught’s armor, they believed that Onslaught was a combination of both Xavier’s and Magneto’s mind, apparently formed when Xavier shut Magneto’s mind down a while back. As the conversations continued and the battle plans forged, X-Force arrived at the mansion to aid the heroes as well.
Recalling the images of Franklin Richards and X-Man on Xavier’s computer screen shortly before his final transformation into Onslaught, the villain apparently targeting them for their shear unlimited powers; Cyclops ordered that X-Man stay in the mansion, with X-Force keeping an eye on him. Fearing for the safety of Cable, another powerful psychic mutant and genetically almost Nate Grey’s twin, Storm set out to search for him. Knowing that Magneto was still out there somewhere on Earth, and with a desperate need to find him to learn more about Onslaught, some of the Avengers and Gambit set out to search for him via Cerebro. In the meantime, the other half of the Avengers, along with Bishop and Iceman, would try to warn the Fantastic Four of the imminent danger. Wolverine, meanwhile, had a hunch to play out to find information about Onslaught, and set out on his own. Cyclops and Phoenix, decided to take a small squad with them to Muir Island, where they were to rendezvous with Moira MacTaggert. As soon as Excalibur had been informed of Xavier having become Onslaught, and thus a traitor to the dream, Moira revealed that she knew of some way to defeat him - something called the Xavier Protocols.
The Most Evil of Plots
Meanwhile, the “Dark” Beast had taken Onslaught deep into the Morlock Tunnels, where Onslaught could hide and recuperate. He was still a little weak and needed to regenerate his powers to full strength before making his next move. Onslaught grew impatient of Dark Beast’s constant jokes and made him pay for it through torture, though as the Dark Beast had promised him more lackeys, he deemed him useful enough and kept him alive. Onslaught couldn’t wait, and was certain that it was only a matter of time before the entire world would be his. At the same time deep inside Onslaught’s heart, Charles Xavier quietly raged against the dying light of his dream.
However, while all this was taking place, another sadistic plot was on its way to realization. The mighty Apocalypse rose up again from his sleep, and was contacted by the cosmic being, the Watcher. Because of the Watcher’s presence, his race usually sworn to non-interference, Apocalypse realized the magnitude of the events that were unfolding. The Watcher wanting Apocalypse to witness the upcoming war could only mean that it would soon be the end of the age of the heroes, and that most importantly…he above all would survive it. The only one who could really be danger to that goal was Cable, but fortunately for Apocalypse, Onslaught himself was already in the process of eliminating that threat. [Uncanny X-Men #335]
It turned out the villain had found himself another lackey, by mentally gaining complete control of the Hulk. He used the green monster to make sure he would kill Cable, who had just woken up after his battle with Post. The two fought a hard battle, during which Cable telepathically tried to bring Bruce Banner, the Hulk’s human side, back to the surface, but that only resulted in more danger. The Hulk switched personalities; the gray Mr. Fixit version of him gaining dominance, furious and out of control. The Hulk punched Cable so hard that even his techno-organic virus got the upper hand, and Cable was dying. 
Luckily, he was rescued by the timely arrival of Storm. The two combined their powers to blow the Hulk away, and Cable managed to pull off a psi-blast strong enough for another personality change. This time, the Hulk was green again, but in his rampaging “Hulk Smash” mode. In this savage state, the Hulk was more than Storm and Cable could handle, and they were both knocked out. Regaining consciousness, Cable found himself a captive of the Hulk, and on the way to Onslaught. He then used his telepathy for a more subtle approach and entered the beast’s mind, reminding Bruce Banner of things dear to him like his wife, Betty. When Storm too recovered, the two heroes could eventually beat the Hulk and free him from Onslaught’s control. Storm struck down the Hulk with lightning, actually causing his mind to shut off, and Cable helped it to properly “reboot“ with Bruce Banner in control. The stunt had almost ended his life, but Storm and Cable could return to New York City with the Hulk on their side. [Cable (1st series) #34, Incredible Hulk (2nd series) #444]
Elsewhere, a vile third party entered the scene. Discovering that his eternal enemy, Apocalypse, had awakened, Mr. Sinister realized that it was time to collect what he had been waiting for a long time. Tracking down Threnody with his Marauders to New York City, Sinister learned that X-Man was at the Xavier Institute. Once there, Sinister discovered the mansion empty except for X-Force and X-Man. Taking down Siryn and Caliban, Sinister then confronted the rest of X-Force, whom he easily dispatched, before filling in X-Man on a horrible secret. Nate was the one who gave Onslaught a physical form, after he pulled Xavier out of the psychic plane and into the physical realm once. 
In short, X-Man taught Onslaught how to become a corporeal form. Not only that, Nate also found out that, just like Mr. Sinister had orchestrated Cable’s birth to gain the ultimate weapon against Apocalypse, he was created by the Sinister from his own timeline. Still in shock over this revelation, Nate’s powers were seemingly turned off by the mad geneticist. X-Force tried their best to keep Sinister from X-Man, and they led him through a wild chase through the ruined mansion. Along the way, Nate picked up some of Cable’s Askani teachings from Sunspot’s mind, enabling him to overcome Sinister’s mental block of his powers. However, X-Man fell into a trap when he probed into Sinister’s head, for the scientist deflected the psionic energy and turned it into a blast against the heroes, knocking them out. He then grabbed his prize - Nate Grey, and proceeded to leave. [X-Man #10, 18, X-Force (1st series) #57]
Gathering all the Players
The group of Avengers that had departed to search for Magneto, along with Gambit, made use of Cerebro to locate a signature matching Magneto’s somewhere in Virginia. During the flight there, the Scarlet Witch went down memory lane, and told the others how badly Magneto used to treat his members of his Brotherhood of Evil Mutants, just to prove that he was the master and not they. 
Upon their arrival in Virginia, the group found not only a man who seemed to be Magneto, albeit much younger and now calling himself Joseph, but also Rogue who was accompanying him. Noticing that Rogue and Joseph seemed to be rather close, Gambit became confused and demanded to know what was going on. The Avengers called Magneto by his name, but Joseph didn’t remember it. Instead, Rogue fought the Avengers, who first struck Joseph and told them to keep Joseph’s former identity as Magneto a secret, because she didn’t want to risk him remembering his past life and returning to his old ways. Regardless, the fight went on, mostly due to Quicksilver’s rage, and at one point Joseph lashed out with his powers against the Scarlet Witch. When she screamed in agony, he immediately stopped, and reached out his hand as a friendly gesture. This act convinced Wanda that Joseph was indeed a changed man, and she used hex bolts to separate the combatants. The Avengers respecting Joseph’s amnesia, the heroes took him and Rogue aboard their Quinjet, and returned to the other heroes in New York City. [Avengers (1st series) #401]
In New York, the remaining Avengers together with Bishop and Iceman, sent a warning to Four Freedoms Plaza to warn the Fantastic Four of the situation, and Xavier’s interest in Franklin. Unfortunately, when Scott Lang, aka Ant-Man answered the call, he was taken out by Onslaught before he could warn any of his teammates. In the guise of Charles Xavier, Onslaught himself arrived at the headquarters of the Fantastic Four, demanding that Sue and Reed handed over Franklin to him as he should be trained in his mutant powers at Xavier’s school. 
Unbeknownst to all though, Onslaught had already entered Franklin’s life as his imaginary friend, Charlie, in an attempt to gain the boy’s trust, and eventually his reality warping powers. When Reed and Sue refused to hand over Franklin, the beast showed his true colors, and attacked the world’s premier super team. Thanks to Crystal’s teleporting dog, Lockjaw, the Avengers arrived as well, but they were not strong enough to stop Onslaught. While the Invisible Woman and Bishop used their powers in combination, and caused Onslaught to briefly revert to Xavier, the villain made quick use of the heroes‘ hesitation. In the instant he changed back to Onslaught, he defeated all the heroes and managed to kidnap Franklin. [Fantastic Four (1st series) #415]
All the while, the remaining X-Men had had made their way to Muir island, where Moira MacTaggert led them to a special chamber underneath her lab complex. Nobody but Xavier had been inside before, and once they entered the crypt, a computer system activated itself and a holographic image of Xavier showed up. It explained to them that apparently he must have become a threat to the world for Moira to contact his students and lead them here. Always having feared such a thing happening, Xavier had done a lot of research on how to shut down his psychic powers, and he made some blueprints to the solution - some special psi-proof armor. In fact, this was not the only file store in the crypt - there was a whole set of Xavier Protocols, each having information how to kill a certain member of the X-Men or one of their spin-off teams, in case they should become a threat. The X-Men were devastated to find out that during the many nights in his study room, Xavier was trying to figure out ways to kill his students, but as time was of the essence, they quickly downloaded the blueprints for the psychic armor and returned to New York. [Excalibur (1st series) #100]