In the DC universe, Superman can be treated more like a god than a superhero, but when it comes down to it, there are plenty of ways to beat Superman. Superman has a number of weaknesses that make him susceptible to a variety of different strikes. Powerful magic users, telepaths, and anyone with a chunk of Kryptonite stand a reasonable chance to take down Kal-El. While a number of heroes and villains in DC's multiverse have defeated the Man of Steel, the better question may be who can beat Superman in Marvel?
Comic fans generally recognize Marvel as a company that tells stories about heroes who are real people and DC as a company that tells stories about borderline deities. Still, there are plenty of overpowered Marvel characters that could stack up to Superman in a fight. But why would a hero from Marvel need to take out Superman anyway? Well, sometimes the big blue boy scout is a bit of a jerk.
Fans of Superman will know that he's always struggled against chaotic magic wielders capable of altering reality - we're looking at you, Mister Mxyzptlk. And, unlike the fifth-dimensional imp, Scarlet Witch won't be banished into another dimension if she has to spell her name backward.
Scarlet Witch can alter reality in any way she sees fit. This was shown in House Of M, wherein Wanda altered the entire world and brainwashed its inhabitants to think the world had always been how she had rearranged things. So, in a fight with Superman, what's stopping her from altering reality around Superman to put him in a room full of Kryptonite or changing the Sun from yellow (which gives him power) to red. Scarlet Witch has the reality-altering powers of a god, and it's by her own goodwill that she doesn't simply take over the world.
Superman's primary (and most famous) weakness will always be Kryptonite. But the Man of Steel is also quite vulnerable to magic. It makes sense for a hero who solves most problems with his physical abilities to have very little knowledge of magic in general. So, Superman would be totally exposed when facing a magic-user of Doctor Strange's caliber.
So, how would Doctor Strange defeat a foe like Superman? Well, there are infinite uses of magic, so, to be quite honest, there are an infinite amount of magical strategies Strange could employ to best Supes. The easiest way would be to take a page out of Superman's Phantom Zone banishment and banish Superman into a dimension he couldn't escape from. Thanks to the aforementioned Phantom Zone, readers already know that Kryptonians, like Zod, have no real way to escape from dimensions they're sent into, so a simple banishment should hold of Superman for a good, long time.
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Superman is vulnerable to telepaths, and Professor X is the most powerful telepath on Earth-616. Professor X became even more powerful since helping found the mutant nation of Krakoa after redesigning Cerebro to take a portable form that constantly amplifies his abilities.
Superman has been shown to fall prey to mind control on many occasions. In one example, Poison Ivy was able to control his mind (and the minds of the rest of the world) through the infection of all plant-based food on Earth. If Ivy is capable of mind-controlling Superman, then Professor X certainly is. This fight would be over before it began; Superman wouldn't have time to land a single punch before the total mental takeover would begin.
Legion is the son of Charles Xavier and one of the most powerful mutants of all time. Legion has dissociative identity disorder, and each one of his personalities has a different mutation and power. Legion has often been described as being a mutant with hundreds of different Omega-level mutations. And, let's face it, one of these personalities is bound to best Superman.
In Legion's most powerful form, he can warp both reality and time. He is described by others as a god mutant, and his power makes him more than fitting for that title. Legion's own time-traveling changed the entire course of the world and led to a reality in which Apocalypse was the ruler.
But, for the sake of variety, Legion also has a personality that gives him the power to turn anything he touches into salt. And, well, Superman couldn't do a lot of fighting if he was turned into salt.