Stan Lee and Jack Kirby's X-Men have provided fans with a wealth of fan-favorite characters since their inception in the early 1960s. However, they're also arguably one of the most famous groups of superheroes to take the most punishment in their vast catalog of stories.
Since the concept of the X-Men is based on an allegory to dealing with bigotry and oppression, many of these stories see their most grueling setbacks stem from non-Mutants' fears of the "other." However, not all of these issues came from external forces like federal governments and international governing bodies. Some of the most crushing events to affect the X-Men also came from rifts among their community.
The Personal Rift Between Professor X & Magneto
One of the X-Men's original tragedies became one of Marvel Comics' most important events. Charles Xavier and (originally named) Max Eisenhardt befriended each other years after the latter's tragic origins as a Nazi-Germany Holocaust survivor. However, their allegiance wouldn't last - at least not consistently.
Charles and Max's worldviews were incompatible in terms of what they seek for Mutantkind, with the former fighting for peaceful equality, while the latter believes they will never be accepted by humans and, therefore, opts for Mutant supremacy and domination. This stark rift in their ideologies sets the stage for the X-Men's fight for justice and against Max/Magneto's Brotherhood of Mutants. Despite this divide, Magneto still maintains an overall friendship with Professor X, though, with his role fluctuating between a supervillain, anti-hero, and superhero.
Nazi-Germany's Persecution Of Mutants
Given the aforementioned ties to Nazi-era Germany and the Holocaust, Magneto's brutal upbringing as a Jewish Mutant in the region can qualify as another one of the X-Men's collective, and original tragedies. With his family murdered, Max would be captured both in German-occupied Poland and then moved back to Germany in Auschwitz.
What he would become as Magneto incited some heinous acts-- like what he's done to Wolverine in the past and using Sentinels against the X-Men - but one of the best ways to write a compelling supervillain is to make them sympathetic. Magneto is a great example of the "sympathetic villain," as someone whose methods are often objectively reprehensible and cruel but have a nuanced backstory to make his madness a logical conflict from a narrative perspective.
Magneto Uses The Sentinels Against The X-Men
While Magneto is one of the most iconic sympathetic villains in comics, one of the many vicious things that he's done was use Sentinels against the X-Men. After Cyclops and Emma Frost established a new base in San Francisco for Mutants everywhere to find refuge, Magneto disrupts the invitation by attacking the X-Men with his cavalry.
This was one of the most diabolical, callous things that he's done from both a literal and symbolic point of view. Firstly, it's a sort of dark irony that someone who claims to be fighting to save Mutantkind with his methods is actively trying to kill many of them. Finally, the Sentinels were originally a government-funded program of Mutant-hunting robots, so for a fellow Mutant to use them against his own is a bleak form of symbolism.
The U.S. Government Funds The Sentinels As Anti-Mutant Agents
The Sentinels are one of the most notorious reasons that the X-Men have seen so many possible timelines involving the Mutants suffering a genocide. The whole Sentinel Program started when the U.S. government provided the funding so Bolivar Trask could create them.
Though, the initial attempt didn't result in the worst-case scenario, as the Master Mold Sentinel broke free and overthrew his creator's sadistic plans. However, things became worse for the X-Men when Trask's son succeeded him and created a deadlier, more efficient generation of Sentinels that got progressively more so at hunting down Mutants with each passing batch. One of the X-Men's best movies, Days of Future Past, featured them in one such alternate timeline.
The Country Of Madripoor Tries To Poisons Mutant Pharmaceuticals Worldwide
Marvel's fictional country of Madripoor serves primarily as a hotbed of low-profile criminals and high-class villains alike. One of the most notable villainous agencies to come out of Madripoor was an anti-Mutant group formed by former Hellfire Club members and a billionaire.
After gaining control over the country's government, the group attempted to poison the sovereign Mutant state of Krakoa's worldwide pharmaceuticals. The goal was to taint the medicine to kill countless innocents around the world to frame the X-Men and Mutantkind for maliciousness against humans. Thankfully, the scope of this mass slaughter was contained, but innocent people still died just for the sake of spiting the X-Men.
American & Canadian Governments Experimenting On Mutants
One of the X-Men and Marvel's best superhero characters is a classic example of the horrors inflicted on the team. James "Logan" Howlett was experimented on in the most famous example of the Weapon X program. The experiments from this effort are what infused him with adamantium to give him his claws, regenerative abilities, slowed aging, and near-invulnerability.
By the time this program evolved from the days of Captain America's Super-Soldier serum, it was moving onto more dangerous efforts en mass on Mutants, creating others like Wolverine's arch-nemesis Sabretooth. The Weapon X program was given even easier access to Mutants to experiment on with the help of the U.S. and Canadian governments funding.