Atlas Institute

One of the three major branches of the Association. Located in the Atlas mountains of Egypt, it is a place where those dedicated to the study of alchemy gather.
Unlike the modern alchemy that rose to prominence in the middle ages, the alchemy studied by Atlas could be said to be the progenitor of magecraft, and an attempt to unravel the truth of the world.
For some reason they are on extraordinarily bad terms with the Prague Association, and even the Clock Tower, the very heart of the Association, keeps their distance. They are colloquially known as the Giant’s Pit.
In order to avoid the “end” proven by their first director, they endlessly create and dispose of weapon after weapon.
There is a saying in the Prague Association: “Lift not the seal of Atlas, lest ye destroy the world seven times over.”
…The reason being that the weapons created there to save the world are ultimately nothing more than tools that will further its destruction.
Though calling it “one of the three major branches of the Association” sounds nice, in reality it is more like an independent think tank. They have been known, on rare occasions, to loan out their alchemists to other mage’s associations and even the Holy Church upon request.
In order to hire an Atlas alchemist, however, one of the written contracts issued by the Atlas Institute is required. Only seven of these contracts were ever issued, and the Atlas Institute considers their recovery a top priority.

Tsukihime Dokuhon Plus Period: Tsukihime Dictionary Revised
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The institute Sion belonged to, and one of the three major branches of the Association. Located in the Atlas mountains of Egypt, it is a place where those dedicated to the study of alchemy gather. Colloquially known as the Giant’s Pit.
Unlike the modern alchemy that rose to prominence in the middle ages, the alchemy studied by Atlas could be said to be the progenitor of magecraft. For some reason they are on extraordinarily bad terms with the Prague Association, and even the Clock Tower, the very heart of the Association, keeps their distance.
In order to avoid the “end” proven by their first director, they endlessly create and dispose of weapon after weapon.
There is a saying in the Prague Association: “Lift not the seal of Atlas, lest ye destroy the world seven times over.”
…The reason being that the weapons created there to save the world are ultimately nothing more than tools that will further its destruction.

MB Act Cadenza PS2 Manual: Tsukihime Dictionary
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The Atlas Institute is an association of magus and alchemists based somewhere in Egypt’s Atlas Mountains. It is also known as the Giant’s Pit.
Of the three divisions of what had once been the Mage’s Association, the institute of accumulation and measurement.
They were a group of practitioners of alchemy, not of the modern alchemy that became dominant since the medieval times, but the progenitor of magecraft, the alchemy that investigates the truth of the world.
They’re not so much as mages as they are individuals with abnormal powers who treat their own bodies like humanoid machines, using them like vessels for working their minds more accurately, more powerfully, more quickly.
They believed that humans are a rare sort of computers with motor functions (the five senses), that we humans are intelligent lifeforms that evolved to collect and analyze information and directly solve the problems created from that as manual labor.
The correctness of this idea was proven unexpectedly in the world of Extra where magecraft died out.
The alchemists of Atlas have poor magic circuits, and did not lead their lives relying on magic power.
As they did not rely on it (or to be more precise, could not), they were able to continue their pursuit of knowledge as disciples of magecraft even after the depletion of mana.
However, for a long time children had stopped being born, and the Atlas Institute, with its old alchemists taking their lives, was at the end of its ropes irrespective of the mana depletion.
All that remains of the Atlas Institute is a single homunculus. The last Atlasian succumbed to disease after creating the homunculus, and only her creations were left in her cave.
The Atlas alchemists disappeared, and their research facilities which were built using unknown techniques stretch out in an underground city which is now, more or less, a giant graveyard.

Fate/EXTRA Material: Encyclopedia of Fate/EXTRA
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An organization of magi and alchemists based somewhere in Egypt’s Atlas Mountains. One of the three great branches of the Mage’s Association. The Atlas Institute holds that the future demise of mankind is inevitable, and works so as to delay mankind’s expiration in every possible way. Even the metamorphosis or retrogression of humans as a species is accordingly deemed acceptable – as long as such measures enable an extension of humanity’s survival. Unlike other magi, members of the Atlas Institute do not pursue the evolution of humans into lifeforms of a higher order.

MB Back Alley Alliance Nightmare: Encyclopedia of Rojiura Nightmare
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Commonly nicknamed “The Titan’s Cellar.”
An association of alchemists located in the Atlas Mountains, Egypt. The institute of aggregation and measurement.
They were originally one of the three major divisions of the Mage’s Association, but they are less a group of mages and more a group of superpowered individuals who treat their bodies as man-machines.
A self-destructive foundation that continuously builds weapons capable of ruining mankind in order to prevent the ruin of mankind. Their only precept is not to reveal the results of your research to individuals other than yourself.
However, as mentioned in-story, any method capable of preventing the ruin of mankind has a high likelihood of also being capable of causing it. That is a fundamental problem with the Atlas Institute and all its personnel, and much like their Mage’s Association colleagues from the Clock Tower with their inability to reach the Root being caused by their attempts to, they are also burdened with a hopeless karma.
Needless to say, the Black Barrel, the Logos React, the rest of Seven Superweapons, and their related inventions all share this same nature.
On another topic, unlike the people of the Clock Tower, the alchemists affiliated with Atlas have little to no Magic Circuits. However, one group of families called The Six Sources of Atlas possess special cells that produce magical energy that functions only within their bodies. These abilities called Traditional Features are mere checkpoints toward Atlas’s goal but the families internally develop them in order to awaken the abilities of their bodies. The Etherlight of the Eltnam family, for example, was initially developed as pseudo-nerves for medical purposes and eventually reached the point where people can use them without necessarily being an Eltnam, although with some functions restricted (it’s still a fact that only the family can use it to its true potential). Additionally, Sion Eltnam Sokaris has a power named Transparent Body, but you’ll have to read the story to understand just how compatible with Etherlight that makes her.
Oh, “why do only the members of the Six Sources have these cells?”, you ask? See, the Atlas Institute began with…

TYPE-MOON BOOKS material: The Adventures of Lord El-Melloi II Glossary