The purpose of the Atlas Foundation is to as some of them put it “Science the shit out of everything”. Atlas brought together the most brilliant minds in the multiverse with most of them at the age of one processing information at the speed of a supercomputer. Thus they believe that by analyzing everything the multiverse has to offer, they can be as powerful as supernatural beings.
There is a reason why they call themselves the foundation of humanity. Checking a majority of timelines one can see it is dominated by people with supernatural abilities. In these worlds humans are often underneath the supernatural either through literal subordination or humanity knows not of the supernatural. Thus through the power of science they wish to prove the common theme in the multiverse wrong. That humanity needs not the supernatural to progress itself. That humanity can strive against the lone dark cold. That humanity will survive and overthrow the supernatural. This leads to why they call themselves Atlas. Atlas was a titan who held up the sky and just like him this organization will hold up humanity.
Then there is the last purpose of Atlas and by far the most important. The creator of the organization known as the Hidden Man told his three disciples of the end of the multiverse. How the multiverse ends he left unknown. Thus the three were tempted to create Superweapons capable of destroying a being who could destroy the multiverse. However they became aware that the weapon could be the very thing which would destroy the multiverse. Thus all Superweapons created must stay in Atlas’s Vault to avoid the potential of it destroying the multiverse.
The beginning of Atlas is only known to a few select people. Even less know of the man who started it all. The man was a man of science. In fact, he was a primordial human relative to the entire multiverse. He was known by many names. The Inquirer. The Progenitor of Science. The Thinker. God. Kami-Sama. He earned those titles as he was the first being to think about reality as he created a set of rules known as the Scientific Method. He spread this idea across the multiverse. Thus the idea of Science sprouted. Press skip a couple millenia or so came humanity use of science. Out of all the beings in the multiverse humanity fascinated him. A species with no special abilities. He perceived it as impossible for them to succeed. Yet……..they did. Humanity grew in power. Not even close to the others in the multiverse but beyond his expectations. Thus he looked into all possible alternate universes for the smartest humans relative to his current position in time. He found them. The Three Disciples.
The first he found in Ancient Egypt. She was a young woman who often pondered the world around her. She was several light years ahead of her times. Her name was Isis. She was capable of great feats of science which was often mistaken for magic. She was capable of making chemicals capable of healing someone an inch away from death. Her chemicals were used to put the king of her time Osiris in a state of life and death. She gathered up all his body parts and applied an elixir which meleded the body parts together. She then forced the dead body to drink another elixir which restarted all his bodily functions such as cell division and blood flow. Thus she managed to revive someone through the power of science. Furthermore she had skill with technology capable of building entire guns which could shoot faster than a railgun. She used this skill to create entire portals which could be used to go to different spaces in reality.
This was more than enough to get the eye of the Hidden Man. Thus he came down in the form of a sickly old man to test her. You see he had suspicions not believing anyone was nice enough like her. He offered her ultimate knowledge as long as she killed her father. Now Isis was no idiot and examined the situation in front of her. After sufficient analysis she believed him. So she created a small snake homunculus to peacefully kill her own father. The Hidden Man was not angry but rather intrigued by her desire for knowledge and took her under his wing.
The second was also found in Egypt. He was born in a time before Moses' supposed date of birth. While the woman Isis focused on the making of powerful elixirs and chemicals, he focused on purifying and perfecting matter. This man considered fake to some is Hermes Trismegistus. The Father of Alchemy. Contrary to popular belief, he did not perceive the world in the four classical elements but rather used it to teach his students in a simpler way. He perceived the world as Atoms which was split into protons, neutrons, and electrons. Using this knowledge of the universe, he has a goal to create a Philosopher's Stone. He succeeded in his endeavors and managed to create an object capable of removing the impurities from a certain material. He would use this in his further endeavors as seen when he used it to recreate the whole Nile River.
Thus he managed to get accepted by the Hidden Man who tested him through giving him a choice to destroy the stone and come to him to go beyond his limits. Or reject his offer keeping the stone. Keep in mind the stone took over 50 years to make. He first wanted to see proof of what he could do if he went beyond his limits. The Hidden Man said that he had to take a leap of faith. So he destroyed the stone…...but kept the fragments which immediately were attracted to each other thus rebuilding the stone. One would think the Hidden Man would be angry to be deceived like that but he was rather pleased by Hermes’s ingenuity and accepted him as the second disciple.
The last disciple was found in Britain. More specifically London. This one was the one who interested him the most. HIs specialty was not any product he could make. He didn’t make miraculous miracle fluids capable of raising the dead. He couldn’t create water from the air. The thing special about him was his ability to think. He was a philosopher and a mathematician of the highest level. He would stay in his office working on equations trying to decipher the reality around him. He wrote several controversial works. An example was Science and the Occult: A Matter of Perspective. This got massive backlash from the church, occultist, and scientist. Compared to the other disciples he was just a thinker. Until he pulled off something huge. Something that was the lowest possible probable outcome that the Hidden Man saw no point to keep in mind. He found the formula…...to Life and Death. He tried publishing this work but was quickly rejected and was sent to be burned on a cross.
As he burned he uttered just one word. “.....Die” This one word caused everything to collapse. Through his now new power over life and death…..he killed everything. He killed everything. He killed every living thing on the planet. No….he killed the very idea of life. He killed the concept of good and evil. The only thing that could be classified as living was himself. The Hidden Man was smiling through all of it. He was sad that the planet that he was visiting died but was more fascinated by the man. The man immediately accepted the Hidden Man’s offer. Oh. The name of this man you ask?His name was John Ironwood.
The three disciples immediately hit it off once they interacted with each other becoming almost like family. Hermes and Isis would come up with different combinations of chemicals together with Hermes helping Isis even more, teaching her how exactly the universe worked on a subatomic level. Hermes and John would often have philosophical debates with John teaching Hermes of different perspectives on reality and Metaphysics. Isis and Hermes taught John to start thinking about the physical reality in front of him. All in all, they each aided each other.
Now to go into what exactly the Hidden Man wanted with the three. The man decided to teach them to push them beyond their current limits. Rather than teaching them facts and ordering them to memorize them, he put them in different universes allowing them to take live scientific studies. An example for Hermes is that he was put on a planet which was mostly made of Nitrogen; both in the air, the ground, and as a liquid. However people could still survive on the planet. His job was to figure out how. By figuring this out he could make his homunculus able to survive such a condition. Isis was sent to a world where Electromagnetism did not exist. She was given the necessary equipment to survive such a space and learnt how they used Gravity and the Strong Force to create technology. Lastly John was sent to a world where people’s perception of reality could enforce visible changes on how it works. Thus his knowledge of Metaphysics increased. The man continued these “lessons” helping each of their knowledge of science grow.
Then after a couple thousand years or so he told them of a phenomenon known as Ascension. He explained this phenomenon as the multiverse rejecting them as normal humans for humans could not do the feats they can now do. Could normal humans just by thinking and decoding the universe have the authority of a god? Could humans harness the power of the big bang? Could humans create technology capable of creating a galaxy? No for that is outside normal humans. They were in the middle of the process. It would be too much to explain such a process. I would need much more time to go into the intricacies of this wonderful process. They later ascended.
He sent them out all across the multiverse looking for more students but not for himself rather the Disciples would teach them spreading the wonders of Science across the multiverse. Before the Hidden Man left he told them that the multiverse would end before vanishing.