First of all, this a far-fetched theory.

So, please, take it with a grain of salt, aight? But still, feel free to read this and think.

My theory is that the mutant gene has been a part of humanity since the dawn of time. However, that gene has remained dormant except when activated by an outside source. The first example of this is contact with an Infinity stone, which is what happened with Quicksilver and Scarlet Witch. The second is Quantum Realm manipulation, which is what happened to Ghost in Ant-Man and the Wasp. Two other examples have been seen on Agents of SHIELD, which are Absorbing Man and Blizzard, who gained their powers in freak accidents or genetic experiments.

However, Wolverine, Professor X and Magneto already exist due to the Weapon X program, which discovered the mutant gene after experimenting on a Canadian soldier during World War II (Wolverine). They also experimented on one of their scientists' unborn children (Magneto). Professor X, meanwhile, created a Quantum Realm device as a teen, and gained his powers when it literally blew up in his face. The only reason mutants haven't been referenced is because there's so few of them.

But that changes when the Avengers use the Quantum Realm to reverse the effects of the Thanos snap. The people trapped in the soul stone (that's also a theory, but it's 99% likely to be true) come back, but half of them have powers, which means that a quarter of earth's population now has powers. This leads to a large social rift and the mutant population splitting into two separate factions: The X-Men, led by Professor Xavier who value unity with humans, and the Brotherhood led by Magneto, who hate humans and believe themselves superior to them. Scarlet Witch is one of the most powerful mutants, and people start hunting her and trying to kill. Pretty soon, reality becomes hard for her to handle and BOOM! House of M and Avengers vs X-Men.

What do you think of this theory? Should Marvel use it? Comment!

So, kind of similar to metahumans?

Yeah, totally! But on a much, much grander scale and with better SFX.