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Per wiki policy, Spoilers Off applies here and all spoilers are unmarked. You Have Been Warned.

The brain's Magic Calculation Area also contains common sense.

This is why so many magicians are crazy bastards. Their Areas are so filled with emotions and magical potential that they just don't have room for sanity. The generations of breeding meant to maximize magic power and nothing else made it worse. They're like chihuahuas, except it was their sanity/magic ratio that got skewed over the generations and not their body size.

Analysis is Tatsuya's Origin
Onwards here be facts (and possible unmarked spoilers):

1) Magic is hereditary, there are pure-blood families who cultivate magic affinity:

Nasuverse: Tohsaka, Matou, Einzbern, Aozaki, and many others.

10/100 great families in Rettousei

2) Heroes who have no heritage and also have troubles with whatever is considered normal and usual:

- Emiya Shirou is a first-generation mage, unable to do even simpliest "Read item's inner structure" magic without completely draining himself.

- Shirazumi Lio is a normal high-school student, who is constantly dissatisfied with his life, feeling that it's not normal for him.

3) Origin is the concept that gives original birth to one's soul, and empowers it (not unlike True Vocation/Mission/Purpose of Existence)

- Shirou being "Sword", his only true magic is creating a subdimension filled with a near-infinite supply of copied legendary weapons.Other applications, from easiest to hardest, include: instant analysis and recreating legendary weapons at one glance, copying common items, reading common items' structure.

- Lio, being "Consumption", was always born a predator, and once happened to be born as a human. After understanding his true idea, he began killing people and eating them, getting his contract with life back.Though, superhuman speed and power, 10-meter jumps and an ability to catch a thrown knife in the air with your teeth and SHATTER IT also aren't bad.

The whole idea of the Origin is, like Taoism, teaching us that finding our own path and following it will make us infinitely more cool and powerful.Transcendental & great!(Even if your true path is murder and cannibalism. Less cool for a moral, but still.)

4) Here in Rettousei we have a protagonist whose only true inborn ability is intercepting any command sequence in existence.Further applications include: immediate understanding of any magic, even unfinished, disrupting any magic, a need to reinvent usual basic magic spells from scratch every time.

Thus, Tatsuya's main skill is actually his original soul capability, and he'll probably either evolve it up to Reality Marble (his own subdimension world with its rules), or understand it deep enough for it to rival Great True Magics (which include Resurrection, Creating a Soul, Travelling to Parallel Worlds, Time Travel, Denial of Nothingness, Destruction of Everything and so on.)

Tatsuya is God!
Self explanatory image

Tatsuya's True Ability
Miyuki feels the way she does, because she was decrypted.

Miyuki is Tatsuya's daemon.
The "operation" used to subdue Tatsuya was similar to intercision, except that the Yotsuba altered it so they could hold his daemon for ransom instead of making him slow and passive (bad traits in an assassin). Miyuki settled into human form from the trauma of it, which also blocks her previous memories, so she believed the Yotsuba when they told her she was a truly human child.

This explains why the Yotsuba forced Miyuki to stay in close proximity with Tatsuya, why she hates being touched by men so much (daemons are partly an embodiment of their person's sexuality, after all, and he is heterosexual), and why she mentally short-circuits when thinking about certain 'facts' the Yotsuba have told her- she's repressing the truth.

Consider this quote from The Amber Spyglass:

Kirjava: I have no name. I did not know I was born until I was torn away from his heart.

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