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In both the comics and the MCU magic and science is all the same thing. There IS only the manipulation of reality and you can do that by what lay people would call "magic" or "science", but it is all the same thing. In the comics magic is specifically a science based power: it is the psionic manipulation of reality.

In both the comics and the MCU anyone can learn to manipulate reality with their mind. It takes time and skill and ability just like learning any other complex thing. Not everyone can advance to all powerful, but most can learn and use a little power.

We see this is the whole first half of the Doctor Strange movie and roughly 1,000 marvel comics. And the MCU has plenty of examples of magic/science being the same thing. Thor movies make this point a couple times.....and remember in the Avengers when Iron Man(Science) absorbs and uses Thor's(Magic) energy blast?

"Witches" are not exactly new to the MCU, as the Doctor Strange movie DOES show at least a couple hundred magic users world wide.

Wanda...is complicated in the comics, plus there have been so, so, so, many retcons, rewrites and the childish "I write what I want and ignore everyone" spam.

Comic Wanda:

So..."classic Wanda" before all the 2000's "lets change everything everything everything more" is a Mutant. So in Marvel a Mutant is a person born with an unique psionic ability to manipulate a bit of reality : shoot out eye beams, regeneration, control weather, and so on. Wanda was born with the mutant power to manipulate probability: to make 'rare' things happen. Wanda could for example make a foe trip or make a gun misfire. For the most part Wanda can't control what happens without extreme will power and focused thoughts.

At birth Wanda was also enchanted by the demon Chiton to be a favorable host body.

In the comics Wanda never had any skill for magic and could not cast very much magic at all. But she did learn lots of skills such as concentration, focus and other mental abilities that magic users use.

A last bit: In the comics a race known as the Celestials altered lots of races, including humans, a million years ago so that they would have the potential to manipulate things and become super human, use magic, or be a mutant.

Putting it all Together:

A couple Infinity Stones....at least the Power, Time and the Reality stones have been on Earth for a while in modern times. Though when we talk about even just a million years, a stone can cover the distance of the whole multiverse and back.

As we have seen Infinity Stones can "awaken" or "enhance" the potential power a person might have........and so it stands to reason that the "potential'' was created by an Infinity Stone.

So this makes the Infinity Stones created the potential for humans to become super human, use magic, or be a mutant.

This explains all the pretty colors that the witches are using: there "magic" is based on the "potential infinity power".

So MCU Wanda is born a with a "potential to use magic" and be a Witch. Though only a slight ability....like many people. When she was exposed to the Stone, it accelerated/advanced/awakened her power.

That seems to be the semi offical way of things right now.....but for one more twist, Wanda might ALSO be a mutant with the power to alter probability. Making her a unique mesh of powers.