Save the Hostages
Joseph was hit in the blast and fell, unnoticed by all except one. Xavier saw it, and while the heroes fought, he crawled to the man he considered to be one of his oldest friends. Luckily, Joseph was alive and well, which Xavier was glad to see. Amidst the battle, the two had a talk, and though Joseph could no longer remember their former friendship, he felt that Xavier was the best friend a man could ever had.
Meanwhile, Nate Grey and Franklin were discussing their situation deep within their prison inside of Onslaught, while watching the events unfold outside their captor. Nate gave into despair, but Franklin remembered that Xavier told him to fight Onslaught. However, he wasn’t strong enough alone, but maybe if he and Nate worked together they could escape. Seeing so much courage in such a young child, Nate used their powers to free the bonds that were binding his and Franklin’s hands, and successfully established telepathic contact with Cable. Being more or less Nate’s genetic twin, Cable quickly found a way to tether them psionically, meaning giving them a path to escape once Onslaught got destroyed, but he needed Xavier’s help for that. However, since Xavier’s powers were gone, Cable suggested that he go inside Joseph’s head, and use his magnetism to nudge the electrochemical barriers in Xavier’s brain. At first, Xavier was against it, but Joseph was in since he wanted to save the two innocent lives, and at the same time hoped to make up for some of the bad things he supposingly had done as Magneto.
War Makes Strange Bedfellows
At the same time, the heroes had to face the side-effects of Franklin’s powers. Onslaught made the young boy unwillingly create a second sun, causing the gravity on Earth to go out of balance. With the heroes‘ heavy hitters like Thor, Storm and Crystal already busy trying to keep the gravimetrical forces contained, it was Dr. Doom of all people who came up with a plan to bypass the forcefield that Onslaught had created around himself. He suggested for Rogue and the Vision to combine their powers, the Avengers phasing into Rogue, hereby merging with her which at the same time augmented her already titanic strength and damped her absorbing power. Wolverine pierced Onslaught’s field with berserker rage, and Giant-Man and Namor held the rift open long enough, to allow a moment’s passage for Rogue/Vision to fly into. Everything went according to the plan, and they went in at full force, but Onslaught didn’t even move one bit. Observing the battlefield from the sidelines, Reed Richards noticed something odd – not only had Onslaught not been hurt by the attack, his armor had expanded as if the creature inside had grown.
Although the Vision ended up badly injured after the blow, Doom’s plan showed at least a partial success, with Onslaught’s force barrier fading. This left him open for attack by the other heroes. Onslaught desperately tried to maintain control, but had the hardest time doing this task. The heroes saw their chance. The Hulk volunteered to do the job, but believed that he was only powerful enough if his human mind of Bruce Banner was shut down. He convinced Phoenix to turn off the only force that could control the savage beast. Phoenix complied, and the Hulk regressed to his old self, and only thought of smashing things. He confronted Onslaught single handedly, and the two titans fought each other. Every blow unleashed by the jade giant unfettered more of Onslaught’s might, and Earth’s heroes could do little but witness the battle and try to not let themselves be knocked over by the psionic cyclone released by Onslaught. They knew with growing certainty that this was their last battle.
Torn Apart
Onslaught kept on loathing about how neither humans or mutants could defeat him, which got the Hulk only more mad, for he felt left out – him being neither human nor mutant. In a fury, the Hulk’s body enlarged and so did his fists. The Hulk gave Onslaught a final punch in the face, which was more something of a nuclear blast! 
Once the smoke cleared, the heroes could not believe their eyes. At the battlesite, they found Bruce Banner’s human body lying right next to the unconscious form of the Hulk! How that was possible, nobody knew. Also, there was the Onslaught’s cracked armor, apparently empty.
The heroes already cried victory, but that was hardly the case. Onslaught was no longer a physical creature who could be bludgeoned into submission. Now he was thought itself; he was perception! The heroes didn’t understand what Onslaught was saying, but one man did. Reed finally realized what a mistake they made. He explained that the armor was just a shell. Inside, Onslaught had been evolving all along, and this psionic entity before them was his final form - pure psionic energy, ready to spread worldwide, and the heroes had left themselves with no way to attack him, since they could no longer touch Onslaught.
The Big Sacrifice
Thor understood what Richards was saying: they needed a vessel to contain Onslaught. Without any thought, the Thunder God flew into Onslaught’s energy form and sacrificed himself, in hopes that his mighty body would be enough to absorb Onslaught. 
Thor landed inside Onslaught’s body and screamed in pain, it didn’t work the way he thought. Reed believed that the plan was useless if Thor did the job alone, for he didn’t have enough mass. That was all the other heroes needed to hear. Making their final goodbyes to each other, they jumped into Onslaught’s energy form one by one, effectively weakening him. The Thing and the Human Torch, most of the assembled Avengers, Iron Man taking Dr. Doom along against his will, even Bruce Banner‘s human half – they all entered Onslaught and bound him to their combined mass.
The atmospheric changes around them told Mr. Fantastic that the plan was working, but still more mass was needed – though not every mass. When Quicksilver, Crystal and Wolverine rushed to jump into Onslaught next, they were held back by Reed. He explained that since Onslaught began life as a mutant, a mutant genetic pattern would give him the perfect means to live again! The Scarlet Witch seemed to be protected by one of her Hex spells when jumping in, but Reed didn’t want the rest of the mutants to dare make contact with Onslaught. It was up to the human heroes to do the job. Quicksilver felt a bit relieved, until he realized that this wouldn’t exclude his wife Crystal, an Inhuman, from giving her life. Using her elemental powers to blow her husband away, she too entered Onslaught. As the only non-mutant heroes left, Mr. Fantastic and the Invisible Woman ordered the X-Men to give everything they had to blow Onslaught out of existence once they had followed the other heroes. Holding each other‘s hand, the Fantastic Four’s couple then threw themselves into the belly of the beast too.
Hollow Victory
With sorrow, the X-Men did as asked, and used all of their various powers on Onslaught’s new substance. They poured on with all their powers and everything they had, and eventually the glowing mass before them began to collapse. Meanwhile, Xavier and Cable successfully entered Onslaught’s inner being and tried to pull out Nate and Franklin the way they had discussed. At first, Nate didn’t trust both men because of bad past meetings, even reminding Xavier that the being all around them, this Onslaught, was both of them combined. However, Xavier would not give up, and eventually Nate grasped the hand reached out to him. Just as Onslaught’s essence dispersed, leaving nothing but a huge crater, Nate and Franklin fell out of the inferno that was Onslaught. However, there was no sign other sign of life where Onslaught was; no other hero who leapt into the beast survived. 
Still in shock, Franklin was confused about the fate of his parents and family, but knew that they were gone. Xavier embraced the boy and promised that the child would see his family again one day. While the X-Men stood in the remains of Central Park, nobody but Franklin seemed to notice a small, blue ball lying nearby.
Blame it on the Mutants
Nate took Xavier to look over a devastated city. They sight before them saddened them, and Nate regretted not having met the fallen heroes much earlier. Their common mourning allowed Nate Grey and Xavier to finally get over their past problems, and they showed their respect for one another. Naturally they were not the only ones to review the day’s events. The Watcher had recorded everything that happened, and for Apocalypse it seemed like order was restored. Onslaught being destroyed put mutants in general (and himself in particular) back on top of the ”food chain“. [Onslaught: Marvel Universe]
With nothing else to be said or done, the X-Men returned to what was left of their destroyed mansion, inviting Quicksilver as he had to deal with the loss of both his wife and sister. 
Naturally Xavier felt ashamed, as he considered himself responsible for Onslaught’s existence, and there was nothing his students could do to change his view. To him it was almost a blessing when Valerie Cooper arrived to arrest him for the sake of national security, despite the fact that Xavier had lost his powers. The X-Men were ready to defend their leader and Xavier was relieved that his students all believed in him so much, but he wanted to atone for his mistakes and willingly let himself be taken into custody.
Graydon Creed saw the Onslaught crisis as the perfect opportunity to provoke the already bad mutant hatred. He soon even visited the battle field in Central Park and sold his hatred on national TV and to all the local newspapers in an attempt to get votes so that he could become President of the United States, and promised that once he was that, he would lock all the mutants up. [Uncanny X-Men #337, X-Men (2nd series) #57]