Circa twenty years in the past, the Sugar Man crossed over from the alternate timeline known as the Age of Apocalypse. He set up a secret base in the Genoshan mountains and, in exchange for regularly providing him with technology and supplies, the Sugar Man created the so called “mutate bonding process” for the Genegineer, David Moreau. [X-Men Prime, Excalibur (1st series) #87]
It was this procedure that allowed the small island nation to prosper. Soon the law was changed, forcing every Genoshan citizen to be tested for mutant genes. Those tested positive would lose all human rights and were declared property of the state.
In a complicated process, these people were stripped of any free will and turned into mutates, having to use their powers to serve the state. Genetic material was also taken from them to artificially create even more mutates. These barbaric set of practices being nothing else but slavery, the Genoshan government hid the truth from the outside world. They assembled the Magistrates, a specially trained squad of soldiers to watch over the mutant race. Trained in hand to hand combat, the Magistrates had access to a vast amount of High Tech equipment to make sure that no outsiders would be able to get too close to the mutates. A division of the Magistrates referred to as the Press Gang, was formed from willing mutants, serving as an example for the government’s claim that Genosha’s mutant citizens had voluntarily chosen their fate for the benefit of their country.
The X-Men first learned of Genosha when their friend, Jenny Ransome, was kidnapped by the Press Gang. Jenny was a Genoshan citizen, whose family had sent her out of the country after faking a negative gene test for her. The mutant heroes made their way to the island nation and eventually managed to rescue Jenny from the Magistrates’ citadel, but only after she had undergone the major treatment phases of the mutate bonding process. Whereas the X-Men returned to their secret headquarters in Australia, Jenny chose to emigrate to the United States together with her boyfriend, Phillip Moreau, ironically the Genegineer’s son. [Uncanny X-Men #235-238]
Realizing that they had no hope in keeping their secret hidden for much longer, the Genoshan government decided to not wait for the world to take notice, but take a pro-active stance. First, the Genoshan government associated themselves with Cameron Hodge, a known mutant-hater and enemy of X-Factor. Next, they declared the X-Men criminals because of the earlier attack and the “theft of a piece of bio-technology” (Jenny Ransome). Affiliated teams such as the New Mutants or X-Factor were considered “guilty by association”.
The Genoshans then used these accusations to justify launching an attack on Xavier’s mansion. The Magistrates captured a bunch of Xavier’s students. Warlock was eventually killed and Wolfsbane was transformed into a mutate. The remaining members of the three mutant teams infiltrated the island to attempt to rescue their friends, but they ended up being caught as well. If not for some of the Magistrates realizing Cameron Hodge was an even greater threat to Genosha than the mutant heroes, it might have been the end for the X-Men. Once freed, the mutants destroyed the Magistrates’ citadel and the equipment used for the mutate process. [X-Tinction Agenda crossover]
Overseen by the UN, a new ruling cabinet that acknowledged mutant rights was established. Havok and Wolfsbane stayed on the island for some time to help and make sure that the new government kept their promises. However, peace didn’t last for long, as soon many of the mutates on the island became infected with the Legacy Virus. To prevent the disease from spreading, the infected patients were isolated in camps and, once again, the different groups on the island had reason to fear and hate each other. [X-Factor (1st series) #89-90]
Former Acolyte Fabian Cortez took advantage of the situation and fueled a mutate rebellion against the Genoshan government that soon turned into a civil war. 
Besides the fanatics on both sides, a third group consisting of humans, mutates and Magistrates was formed, just as the Avengers and the X-Men got involved. Eventually, Cortez was defeated and the superheroes left, but the conditions on the island had deteriorated to even lower standards than before. [Bloodties crossover] The civil war having destroyed many of Genosha’s natural resources , the island nation soon faced an imminent famine on top of the already existing problems, namely the ever-spreading Legacy epidemic and the various fanatical movements fighting each other.
When Magneto threatened the world with magnetic EMP waves, rendering any technology useless, the UN decided to offer him the opportunity to take over the island nation of Genosha. They believed that the self-styled master of mutant-kind would be too busy with the country’s inner problems to pose a danger to the rest of the world. However, the UN misjudged him, as within only six months Magneto and his Acolytes took control of the entire island and rectified most of its problems. Under Magneto’s forceful rule, the economy prospered again, even though Genosha human population was eventually exiled and forced to leave the island. [Magneto: Dark Seduction #1-4]
With Colossus sacrificing himself to cure the Legacy Virus, the last of Magneto’s problems was solved. Instead of thousands of dying people, Magneto now had an entire super-powered army at his disposal and prepared to conquer the world. [Uncanny X-Men #390, X-Men (2nd series) #111] With most of the X-Men absent or otherwise busy, Jean Grey assembled an interim team of inexperienced mutants to take on Magneto. Against all odds, they were able to engage Magneto in an illusionary fight, while Wolverine and Cyclops secretly entered the island. Eventually, Magneto saw through the deception, but before he could react, Wolverine stabbed him in the gut, inflicting a near mortal wound. With the immediate threat dealt with, the X-Men departed. [Eve of Destruction crossover]
A few weeks later, Xavier’s heretofore unknown twin, Cassandra Nova, took control of a wild breed of evolved Sentinels. Wanting to ensure that humans would become the dominant species, 
she ordered the destruction of the world’s largest concentration of mutant signatures. The advanced Sentinels flew to Genosha and devastated the island, killing the overwhelming majority of the 16 million living on the island, apparently including Magneto who was still recovering from Wolverine’s attack. One of the handful survivors was Emma Frost, who was saved from certain death by manifesting the “secondary mutation” to transform into organic diamond. [New X-Men #115-116]
In the weeks that followed, the few survivors were joined by other mutants who re-settled to the once proud island to honor the master of magnetism and the ideals he stood for. They even constructed a monument to Magneto out of the remains of the Mega-Sentinel that had slaughtered the Genoshan population. [New X-Men (1st series) #132]
Somewhat later, Magneto re-surfaced, although even he himself has no idea how he survived. When Xavier telepathically sensed the presence of his old friend, he arranged to meet with him on Genosha. For once they decided to put their differences aside and to work towards rebuilding the devastated Genosha together. They soon found themselves some surprising allies, old and new, on Genosha’s shores and began to explore the ruins of Hammer Bay. Even though they had to deal with threats from Looters and Magistrates attempting to take control of the island, they began to rebuild and start to search the rest of the island for others willing to help. [Excalibur (2nd series) #1-7]
However, before any real progress could be made, Magneto learned of the Scarlet Witch’s nervous break-down and her ever-growing powers to alter reality. Magneto snatched Wanda from her battle 
with her fellow Avengers and brought her to Genosha, where he asked Xavier to restore the Scarlet Witch’s sanity - but to no avail. The telepath couldn’t help her and, concerned of the threat to reality that Wanda posed, Xavier consulted the Avengers and the X-Men what to do with Magneto’s daughter. Their decision was rendered moot, though, as by the time they reached Genosha reality altered around the heroes - changing into the world ruled by the “House of M.” [Excalibur (2nd series) #8-9, 14, House of M #1]
While reality was eventually restored, it came at a high price, as 90-95% of Earth’s mutant population lost their powers in the process. Just like most of his new Genoshan allies and enemies, Magneto was among the de-powered people, remaining trapped on the island. [House of M #7-8]
Some time later, Quicksilver tried to undo his sister’s actions, and he stole the Terrigen crystals from the Inhumans, wanting to use them to re-power other mutants, just like he had used them on himself. When he arrived on Genosha, Quicksilver promised the de-powered mutants still living to return their abilities. Those who accepted, didn’t listen to the Magento’s warning that the procedure was dangerous, but soon learned for themselves. The Terrigen crystals did more harm than good, temporarily returning the lost powers but amplifying them to an uncontrollable state, resulting in at least one mutant’s death. The Inhuman Royal family learnt of the theft and went after Quicksilver, arriving on Genosha at about the same time as the American military, who wanted to claim the crystals for themselves. During the resulting battle, none of the combatants cared too much about the fate of the Genoshans. [Son of M #4-6]
In the universe, energy cannot be created nor destroyed, and the same held true for the energies of the numerous depowered mutants. Eventually, these energies gathered in the form of an unsuspecting energy-absorbing mutant named Michael Pointer. Dubbed “the Collective” by the Avengers, against whom he then fought, the Collective traveled to Genosha and reached out to the startled Magneto. The Collective attempted to restore Magneto’s powers and convince him to lead the remaining mutants into taking over the planet. To the Collective’s surprise, Magneto resisted and allowed the Avengers to separate the energy from his body and send it into the sun. The injured Magneto apparently died in an explosion, [New Avengers #19-20] and it remains to be seen, who, if anyone at all, is still residing on Genosha.