The Supreme Intelligence, also known as the Supremor, was created more than a million years ago by the extraterrestrial race known as the Kree to help them create a Cosmic Cube like the Shaper of Worlds that their enemies, the Skrulls, had once created. It is composed of the brains of the greatest Kree minds (thinkers, generals, philosophers, scientists, and so on), removed upon their deaths and assimilated by the super-computer in a process called "Supremorization."
Eventually, the Intelligence developed a mind of its own and refused to create the cube knowing the dangers that could be wrought by an evolved Cosmic Cube, which was what had destroyed massive parts of the Skrull Empire.
Despite this, it was allowed to continue to exist to serve the Kree with its wisdom. Its influence eventually grew to the point where it replaced the Kree government, although it has occasionally been deposed for periods of time. Most of the Kree are fanatically devoted to it, and its worship is organized religion.