Unsurprisingly, considering how powerful Onslaught was, and how many heroes not only fought him but paid the ultimate price, the after-effects are quite many, and were felt throughout the entire Marvel Universe. This article is divided in two parts: while this first page describes the experiences of those who were left behind and had to deal with Earth’s mightiest heroes being gone, the second page is about these Heroes being Reborn in Franklin’s pocket universe, and the ramifications of their Return home.
The Mutants and their Enemies
During the crisis, Cable had to battle both his adversaries, Post and a mind-controlled Hulk. These fights caused some heavy destruction to the metal parts of Cable‘s body and, as a result, his techno-organic virus grew out of control. Nathan almost died as the virus spread over his entire system, though fortunately he was found in time by Nathaniel and Franklin Richards, Cannonball, Domino, Caliban and Storm. The combination of Nathaniel’s scientific knowledge of medication and Cable’s inner strength, which was re-inspired by a conversation with his dead son, Tyler, and wife, Aliya, on the astral plane, returned Cable to the living. The techno-organic virus in check again, Cable went on with his life. [Cable (2nd series) #35]
The media blamed the entire Onslaught incident on mutants in general, which, naturally, led to an increase of the public’s fear of mutants. Graydon Creed, the bastard son of Sabretooth and Mystique, saw in this the perfect chance to promote his campaign for the upcoming presidential election. In several public speeches, Creed declared that he wanted to support several new laws, which would have turned mutants into sub-citizens with next to no rights. Graydon was clearly in the lead of the polls, however his political career reached an untimely end when he was shot and incinerated during another of his speeches. The person behind the assassination turned out to be none other than Mystique, who had considered Graydon a disappointment and a loose end in need of being tied up ever since the day she found out that he was not a mutant. [X-Factor (1st series) #130, X-Men Forever #2]
In the wake of Onslaught, Xavier blamed himself of all that had happened, and agreed to be arrested by Valerie Cooper to redeem for his mistakes. However, with the assist of Henry Peter Gyrich, Xavier was placed under the care of Bastion, the leader and founder of Operation: Zero Tolerance, a group that wanted to kill all mutants. 
Bastion tormented the Professor for months to come, just to get more information on the X-Men’s inner workings. However, Xavier didn’t give in to any of the man’s threats and, instead, befriended a fellow captive, the young Mannite Nina, whom he helped to escape from their prison. Just like Creed, Bastion rode the wave of anti-mutant hysteria in order to get his Prime Sentinels started, and he eventually launched an attack against the X-Men and several other mutants, and they even managed to break into Xavier’s mansion. In the end, though, Bastion overstepped his authorities and his Operation was dismantles by SHIELD. It was only several weeks later that Xavier was busted out of his vault and eventually reunited with his students. [Operation Zero Tolerance, The Hunt for Xavier]
A Family Dismembered
The Fantastic Four, having sacrificed their lives against Onslaught, left behind a number of relatives, friends and allies to deal with their legacy. 
Naturally, young Franklin Richards, the son of Mr. Fantastic and the Invisible Woman, was the sole heir, though with him being under age, his grandfather, Nathaniel Richards, was now his legal guardian and, as such, also had to do what was best for the boy’s interests. Shortly after the Fantastic Four’s memorial service, Banshee offered to take in the boy as a ward of Generation X at the Massachusetts Academy, so that he could be with kids of his age. Nathaniel, having more important obligations, agreed, and indeed Franklin quickly became friends with fellow residents Artie and Leech. [Generation X #20]
Because of a loophole in Mr. Fantastic’s will, the government was about to confiscate everything that belonged to Fantastic Four Inc., which included Reed’s inventions. Nathaniel acted rather swiftly, and stashed away the entire equipment of the Fantastic Four in a protective bubble in the Negative Zone, so that by the time governmental officials came to raid the Four Freedom Plaza they found it empty. His work done and his employers gone, reserve member and staff technician Scott Lang, aka Ant-Man II, and his daughter, Cassie, departed to build themselves a new life. In fact, Scott found a new purpose with the Heroes for Hire soon afterwards (see below).
The Human Torch’s ex-wife, Lyja, too left after thanking everyone for the kindness with which she had been met. While originally the Skrull had infiltrated the Fantastic Four by pretending to be Alicia Masters, in whose guise she had married the Torch, she eventually switched sides and redeemed herself. In the end, there was even hope for her and Johnny to rekindle – if not for Onslaught. 
Re-adopting her role and looks as Laura Green, Lyja wanted to find herself a new life and hasn’t been seen since.
The final resident of the Four Freedom Plaza was Kristoff Vernard, aka Dr. Doom II, who had been adopted and re-educated by the Emperor of Latveria to become his heir. With the original Dr. Doom having been consumed by Onslaught as well, Nathaniel Richards accompanied Kristoff to Latveria, where they intended to claim Doom’s castle and the entire nation for themselves. However, they were met with by an army of Doombots. [Tales of the Marvel Universe]
Incomplete Assemblage
While the Avengers had lost a large number of its members, over the years so many heroes had been part of the line-up at one point or the other, that it shouldn’t have been a problem to keep the team going. At least, one would think that to be the case. However, the Black Widow quickly learned that it wasn’t. She had been the chairwoman of the 
group prior to Onslaught, and experienced her share of survivor’s guilt, as she didn’t get the chance to sacrifice herself like her friends and teammates had done. Natasha tried to make up by putting a new team together, contacting a number of former members and other heroes, though nobody was willing to give it a try – each of them already part of another group or busy with other matters. Finally, when the Congress annulled all agreements the Avengers had made with the city and the state (reasoning that none of the founding members with whom these negotiations had been reached were still alive), the Black Widow gave up and shut down the Avengers, only to return to her espionage life. [Avengers Annual ’99]
Obviously, Quicksilver was affected by Onslaught on a more personal basis. He lost both his twin sister, the Scarlet Witch, and his wife, Crystal, at the hands of the evil entity. To help him get over his depression, Pietro was taken in by the X-Men, who tried to cheer him up while figuring out what to do next. At Xavier’s mansion, however, Quicksilver was constantly exposed to Joseph, the man everyone believed to be a de-aged Magneto, and eventually left. Pietro then focused on raising his daughter, Luna, now that he was a single parent, and not much later was asked by the High Evolutionary to lead the Knights of Wundagore for him. [X-Men (2nd series) #57, 59, Quicksilver #1-2]
The trio of remaining Avengers was completed by Hercules. Returning from an adventure in outer space, the demi-god was shocked when he learned of his teammates’ fate and tried to drown his grief in alcohol. With the Black Widow shutting down the Avengers, Hercules briefly joined the Heroes for Hire. However, they had a problem with his way of “mourning” and eventually Hercules himself realized that he would need some time alone to sort things out. [Avengers Annual ’99, Heroes for Hire #3]
In Their Absence
With very few super heroes left to defend Earth’s citizens, other heroes decided to step into the Fantastic Four’s and Avengers’ footsteps. As already mentioned above, there were the Heroes for Hire. Originally only consisting of Luke Cage and Iron Fist, who offered their services for a small fee, this time the group became more high-profile and had a large headquarters at Oracle Inc. Several former Avengers signed up with the Heroes for Hire as well. However, in the end, it remained a service one would have to pay for, which doesn’t entirely mesh with the usual super-hero altruism.
In that regard, the Thunderbolts became the center of attention for New York. Making their debut while the city was still mourning their heroes, the Thunderbolts took the general public in a storm – eager to convince everyone of their good intentions and giving interviews at every turn. They were so well received that the city even gave them the abandoned Four Freedom Plaza to use as their headquarters. However, the team had a dark secret... they were no heroes. It was a scam. In fact, the Thunderbolts were the Masters of Evil in disguise, and Baron Zemo was just luring everyone in a false sense of security, waiting for the perfect opportunity to make his move. What he didn’t foresee, though, was that most of his team actually liked being adored as heroes, and genuinely started to redeem.