The destruction caused a complete overhaul of the organization. Soon enough, it was lead by a toad named VG, who was far more noble than Wolfman. Klumsy, who had always been more of a drill instructor than a leader, was dead. The remaining Questers were less concerned with money than they were good and evil; but their attempt to get to the bottom of things only made things worse.
Zio returned, which was unspeakable. Since the other villians had lost their edge, he became the new head honcho of darkness. Soon enough, he drew together the dishonorable elements of Nintendus into a massive anti-Quester group, which was then named the Quester Hunters. He had some ulterior motive in this; the organization's headquarters housed some sort of secret project of his.
The Questers fought their way to this very base, utilizing a new form of attack called "Trance Mode." In this mode, they had an unfair advantage over their opponents, and lacked control over their actions. It was just the right thing to kill off an endless wall of Oddworld enemies. But as they got deeper, something seriously wrong was starting to happen. They had come to rescue Alys, but Alys wound up rescuing them. She fought Zio to the death, while they just ran. They missed out on their own objective, and were left standing in front of a bunch of ruins with no answers.
The truth was a very bad thing for them. From the rubble emerged a being from another realm... one who surpassed Zio and his dark portal by exponential degrees. A fearsome being named Kuja; he had been secretly following the Questers, and allowed them to have Trance in order for himself to be brought back to life. His home realm had been destroyed, and he had died in his success; but his ghost, seeking more, seeking a place he could control, went through the hole in Nintendus's fabric.
For the questers themselves created this hole; the supporting case wasn't supposed to save the day, and many of ways and weapons were not native to Nintendus. Through this a giant void was created, and through that, most of their unusual new rivals had arrived. This man tricked them into making himself alive again; and he repaid them with death. Once again, the Questers were destroyed; this time, though, the original generation had been almost completely eliminated.
The man went on to destroy their headquarters, but tripped over his own hole; through this hole, Alys had also come back, and she had just the device to stop him: a transformer. He killed her anew, but was trapped in the transformer long before he could deal a definitive end to the Questers.
VG stepped down, having seen his leadership fail just as Wolfman's. A new person was thrust into the bullseye, and it was a former Quester named Metal Man. He was just right for the job; deranged, lacking fear of anything, and good at killing things. He helped establish a new generation of Questers, and continued the work which had destroyed the previous administration: trying to find out how everything was connected. So he brought his new generation and sent them to stop Bowser, who was up to his old tricks again.
They quickly stopped the worn-out tyrant, and for once, Nintendus seemed safe. Then a giant sword descended from the heavens and stabbed into the heart of the castle they were in, destroying both the castle and their dreams. Aboard this massive mechanical vessel was the iron-clad tyrant, Smithy. He went about controlling the Mushroom Kingdom with an endless array of mechanical minions, and for once, succeeded. He also got a Quester to become evil; one Charles Magellean.
This villian brought together yet another round of anti-Questers: these people, all being former Questers, were named the Fallen Questers. Their name was correct to the end; none of them were powerful enough to match the current generation. Smithy's array of satellites proved useless, too; Metal Man continued sending his soldiers to destroy whatever Smithy could use. Charles Magellean came out and drank a powerful poison; this caused him to reveal his true cause and betray the Questers openly. With Smithy and Ivo Robotnik's help, he tried to defeat the Questers once and for all, ignoring the plight of Aribar's trillion-coin mind-control cube (stolen from the evil Skyhigh).But his own machine caused him to lose, and he dissappeared from the radar. Soon, only Smithy remained; he sat atop his fortress and waited, as the Questers walked aboard. They beat him silly and reduced him to cinders, only for his machines to operate a powerful doomsday device, which he had used earlier to permanently erase Ivo from the picture (and nearly eliminate Magellean). This device generated a field of pure darkness, which lead to a realm where all sense was lost. The X-Zone. It was rumored the trip into the realm was permanent; thus, Smithy could get revenge by shredding reality into pieces by sending it here. But one noble Quester, Yurie, refused to let this happen, and sacrificed her own safety to leap into the darkness. There, she found a new foe. The doomsday device was powered by the Master Emerald, and controlled not by Smithy, but Metal Sonic, who had been watching from behind the scenes. He hated the world, and had no plans of helping Smithy. Instead, he just wanted to create endless destruction. Yurie defeated him, though, and destroyed the Emerald, sealing the X-zone and ending his villiany. He returned outside the zone, though, and in a desperate final attack, tried to destroy the Questers. But he was destroyed by Oak's Pseudo-cube bazooka instead. For once, the Questers had truly triumphed! But... the chaos it was about to create would render all of the hard work moot.