The Secret Empire event from Marvel Comics is, unfortunately, most remembered for turning Captain America into a Nazi, but the controversy could have been much worse thanks to a Magneto-starring variant cover. In promotion for the ongoing event (at the time), Marvel released a series of variant covers starring villains with the X-Men supervillain's cover drawing considerable ire given his ties to the Holocaust and the cover connecting him to Hydra.
Marvel's Secret Empire event spearheaded by Nick Spencer told the shocking story of Captain America breaking bad and admitting he worked alongside Hydra, which famously was led by the Nazi, Red Skull. Seeing Captain America - who literally punched Hitler in his debut issue - who was also created by Jack Kirby and Joe Simon, both of whom were Jewish, aligning himself with Hydra, was extremely controversial. While it turned out that Hydra Captain America wasn't the real thing, the entire concept of a Hydra Captain America caused understandable frustration and upset. However, Marvel had another oft-forgotten controversy that nearly made things much worse from the same event, when they unveiled Magneto on a cover for their 'Secret Empire Villains Variants.'
As part of the 'Secret Empire Villains Variants', numerous Marvel evil-doers got featured in their own special comic book covers for Secret Empire. Among them included Arnim Zola, Baron Zemo, and Madame Hydra, who all have connections to Hydra, The Red Skull, and Nazis - while others such as Crossbones, Baron Mordo and Taskmaster were also featured. However, on the fifth issue variant cover, Dan Mora drew Magneto - which caused immediate controversy, given Magneto's history of surviving the Holocaust as a young boy long before the creation of the X-Men.
The drawing itself isn't controversial, but the fact it appeared on the cover of a series about a Hydra takeover had readers immediately concerned. Was Marvel Comics planning on making Magneto join the fight with the Hydra Captain America and betray the ideals and history that were key parts to the character's history? Thankfully, no. Magneto didn't join Secret Empire's Hydra team - but there's little question having him star on a cover for Hydra-led story was a bad idea. Nick Spencer even said the cover was just another variant and had no connection to the storyline.
Ultimately, the potential controversy from making Magneto part of Hydra was avoided, as the variant cover just came out at a bad time. But for an event that made international headlines because how Captain America was changed, there was little question if the Magneto cover came true in the pages of Secret Empire, things would have been much, much worse for Marvel Comics - and understandably so.