Relation between the Beyonders and the Beyonder
The Beyonders originally had only minor appearances in Marvel comics, with cameos in Marvel Two-in-One and a few other issues. Their position and influence changed when Tom DeFalco became editor in chief. DeFalco was unhappy with Jim Shooter's unrelated omnipotent character the Beyonder [singular], and had writer Steve Engelhart retcon him in two issues of Fantastic Four, using the previously-existing race of Beyonders [plural] as the key to the change.
The Beyonders now became the creators of the Beyonder, who shifted from being an individual all-powerful entity to merely one in a series of sentient Cosmic Cubes, along with the Shaper of Worlds and Kubik. Not only that, he was in fact only part of a Cosmic Cube, along with Owen Reece, the Molecule Man. After spending time as a Cube, the Beyonder emerged in a new female form known as Kosmos, and later took the name of the Maker. She was eventually put in a coma by Thanos and then seemingly killed during the events of Annihilation.
A later possible retcon of the Beyonder/Kosmos/Maker's origin by Brian Bendis posited that he was in fact neither a solitary entity nor a sentient Cosmic Cube, but in fact a mutant Inhuman. This retcon is problematic as it does not address the now-lengthy documentation of the relationship between the Beyonder and the Beyonders, the origin of Reece's power (which is also through the Cosmic Cube), or his time spent as a physical Cosmic Cube with Reece. Bendis himself has said the mutant Inhuman storyline was deliberately left vague, and since it has not been referenced since its original publication, it is unknown if it is canon. Since Bendis' possible retcon leaves any new relationship between the Beyonder and the Beyonders undescribed and unclear, and because the canonicity of the Bendis retcon is ambiguous, the Beyonders history below will follow the "original" retcon by Engelhart.
Description and History of the Beyonders
The Beyonders are a race of extradimensional beings of extraordinary power. They have meddled and experimented with the normal multiverse numerous times throughout history, utilizing several alien species and creating the Cosmic Cubes, objects of immense power in their own right. They are named after their dimension, which is beyond normal space and time.
The Beyonders cannot leave their home dimension, and have never been seen. It is unknown if they ever manifest a physical form. When they contact aliens in our universe, they do so through a device called a radical cube. They do not experience time chronologically. Even among the various other extradimensional and cosmic entities, they are a mystery. The Shaper of Worlds, who developed from one of their Cosmic Cubes, says that they wish us well and want us to grow and be like them.
Their dimension has been shown both as a lightless universe and as a universe of pure white. The Fantastic Four were able to reach it using one of Reed Richards' ships, flying through a chain of dimensions starting from the Negative Zone. Kubik and Kosmos (who both derive from the Beyonders' Cosmic Cubes) were able to travel there on their own power.
Experiments with Alien Races
One of the Beyonders' first experiments was to commission the alien Nuwali (from our dimension) to create the Savage Land on Earth, in order to study evolution and change, which are apparently topics of interest to the Beyonders. The Nuwali made an area that was warmed by technologically-enhanced volcanoes and had plants and animals from various eras of Earth's history. They also wrote out "Beyonder" in enormous letters, which were later found by the Fantastic Four. The Beyonders stopped paying the Nuwali in gold after tiring of their reports, and the Nuwali eventually left; the Savage Land later went through various changes due to the influence of various Earth races such as the Deviants.
Having begun by paying other aliens to do their work, the Beyonders moved on to create their own self-motivated race, the Fortisquians, who flew around the universe in ships that looked like comets, observing various civilizations. They would leave a few "Forts" on each planet. They learned that all beings are driven by desire--which was one of the Beyonder's main observations as well. The Beyonders later told the "Forts" to come back to Earth and tune up the Nuwali's volcano-heating devices.
The Beyonders also had some aliens called the Prime Movers of Tarkus, led by Captain Sphinxor, tow the High Evolutionary's Counter-Earth to their "museum." This museum was seemingly in another "space sector" or our universe, not in the Beyonders' native dimension. The High Evolutionary consented to them taking it, but when they arrived, he saw a giant arm, dwarfing anything even he had seen before, take the planet and put it among a collection of other unusual planets. Seeing the enormity of the arm and what it represented, as well as seeing the pinnacle of his accomplishments treated like a mere curio, made the High Evolutionary go temporarily insane. It is unknown whether this arm was a true manifestation of the Beyonders' shape, or whether they have collected anything other than planets in their musuem.
The Cosmic Cubes, Molecule Man, and the Beyonder
The next step in interacting with our universe, and experimenting with the ideas of evolution and desire, was to create the Cosmic Cubes. These are objects of enormous power, able to alter reality on a great (but finite) scale. They are made by releasing power from the Beyonders' dimension into ours, power which is then contained in a small cube-shaped field. These Cubes allow their possessor to recreate reality in whatever way they desire (up to a point; the Cubes are less powerful than, for instance, the Living Tribunal or Eternity). These cubes eventually evolve (or more properly, develop) into sentient beings with similar powers to the Cubes themselves. Three Cubes have developed into sentient beings thus far. The first cube was made by the Skrulls, and turned into the Shaper of Worlds. The group of scientists known as A.I.M., on Earth, created another cube, which turned into Kubik.
The third main cube followed a different, less direct path toward sentience. Owen Reece, a lowly janitor in a nuclear plant, started an accident, triggering the release of the Beyonders' energy. Some of that energy leaked into Reece, and he became the powerful Molecule Man. However, the majority of the energy leaked into another dimension. That energy developed a kind of proto-sentience of its own, and looked back through the pinhole of energy into our own dimension, seeing Reece. As it slowly became self-aware, the energy became an entity, and continued to observe our dimension. Eventually, this entity tried its own experiment, bringing a number of Earth heroes and villains to a newly-formed Battleworld to fight for their greatest desires. In this way it followed the thematic path set by its creators, the Beyonders.
This entity eventually came to Earth, calling itself the Beyonder, and had various misadventures. He seemed to be all-powerful, millions of times more powerful than all the power in our multiverse combined. However, Reece eventually "killed" the Beyonder when he was in a weakened state, and the Beyonder's energy returned to its original Beyond-realm. The explosion of this energy, similar to our own Big Bang, eventually slowed and cooled and turned into a new physical universe.
However, after some machinations by Dr. Doom (who wanted the Beyonder's power), the Molecule Man, Shaper of Worlds, and Kubik ended up in the Beyonder's new universe, and they talked to the Beyonder, who was still self-aware and able to manifest himself physically. The Beyonder finally came to understand that he was not as powerful as he had thought. The cosmic entities of our universe had just been letting him think that he was all-powerful to allow him time to more fully develop his self. His power, along with Reece's, was only the power of one Cosmic Cube which had accidentally never taken on cube form.
The Beyonder and Reece then merged together and became a new cube. Eventually the cube reached the necessary degree of self-awareness, and Reece's essence was sent back to Earth. The cube turned into a new female being, Kosmos.
Thus the Beyonders' interests in desire and evolution came to a head in the self-developed sentience of the wish-fulfilling cubes.
These experiments with the Cosmic Cubes were apparently permitted by the Living Tribunal and other cosmic forces of our dimension.
The Beyonders have not had any significant involvement in our universe since these cubes.