The Beyonder was one of the Marvel universe's most mysterious and powerful super villains, originally conceived as a Omnipotent being from another Multiverse he was later retconned to be a rogue and child cosmic-cube who was unaware of his true nature and caused havoc with his reality-warping powers: this new origin is not set in stone however and the true nature/origin of the Beyonder may never truly be known by any mere mortal - he was the chief antagonist of the Secret Wars series and its sequels.
In the original story the Beyonder is said to be the sum total of an alternate multiverse bigger than the marvel multiverse called the Beyond Realm, the power of this dimension is accidentally uncovered by a scientist in the Marvel Universe, who would become transformed by it into the villainous Molecule Man.
The remaining energies of the Beyond gain sentience and curiosity - using its vast power the newly named "Beyonder" creates a new planet named Battleworld out of pieces of other worlds and abducts a number of heroes and villains from Marvel's Earth and has them battle each other so he can observe the never-ending battle between good and evil.
The "Beyonder" never referred to himself by that name when communicating with his captives, the name was first used by Galactus - the world-eating entity took an interest in the "Beyonder" when he decided the vast energies he possessed could be devoured: this leads Galactus to storm the Beyonder's realm alongside Doctor Doom (who was also after the Beyonder's power but for different reasons).
However the Beyonder is too powerful even for Galactus to handle and thus both him and Doom are banished from the Beyonder's realm. However Dr. Doom would later gain enough knowledge to steal the energies of both Galactus' Worldship and the Beyonder - via utilizing these vast powers Dr. Doom created a 200-mile high golden-tower and gave up villainy, instead focusing his efforts on freeing his mother from the demon Mephisto.
However the Beyonder's sentience possesses the villainous Klaw and manipulates Doom into unwittingly wasting his powers against numerous heroes - which distracted Doom long enough for the Beyonder to retake his powers.
Secret Wars II
The Beyonder would return some time later, his curiosity having been increased by the events of the first Secret Wars he decides to come to Earth and walk among humanity under a number of human guises - however due to his completely alien nature the Beyonder is almost childlike in behavior and must be taught the most basics things of being human, however his curiosity soon sees him getting manipulated by criminals and he uses mind-control to take over the entire planet - he then undoes this when he grows bored of the lack of free-will he has created.
The Beyonder then helps to create Kurse, one of Thor's greatest enemies, has a love affair with Dazzler and contemplates his place in the universe - although in doing so he accidentally inspires the creation of a cult.
While on a train to New York the Beyonder comes into contact with the mutant Boom Boom and takes her to the Xavier Institute, however she becomes terrified when the X-Men and New Mutants both attack the Beyonder on sight - so the godlike being simply transports them both to a world inhabited by the Celestials, he then threatens to destroy the universe in order to fight and seemingly defeat a large number of the godlike aliens.
Boom Boom is understandably scared of the chaos the Beyonder is causing and demands to be sent back to Earth, where she fled to the Avengers to warn them about the Beyonder. Boom Boom would then lead the Beyonder into an ambush by the Avengers, Fantastic Four and other superheroes - although he could easily of beaten them the Beyonder allowed them to defeat him due to the fact he had come to view Boom Boom as a friend.
However the Beyonder would soon decide to help humanity via eliminating Death from the universe - however he resurrected the entity when it became clear that life could not properly exist without death and vice versa, during this cosmic-scaled event Mephisto gathered many supervillains to attack the Beyonder in an attempt to gain his power and gain the favor of Death.
The Beyonder then engaged in a fight with the Puma, believing his only purpose left was to help Puma find his by allowing him to slay him - The Beyonder amplified Puma's powers tenfold and may of even have let Puma kill him, however a careless comment on the Beyonder manipulating everyone by Spider-Man caused Puma to become disheartened and thus the Beyonder survived.
The Beyonder soon after decides all his efforts to improve the universe was a failure and decides to destroy it - he starts by killing the New Mutants and battles the Phoenix.
However, in a classic example of the Beyonder's inability to stay focused, he reconsiders his actions and resurrects the New Mutants, deciding that instead of destroying the universe he shall instead create a mortal body for himself that can still hold all his omnipotent-power - he very nearly succeeds in creating his god-child but is killed by Molecule Man before he can succeed, his limitless power is returned to the "Beyond" and causes a Big Bang that creates a new universe.
According to new his new retcon and the "evidence" uncovered in Secret Wars III the events listed above were not completely real and the Beyonder was simply a powerful reality-warper akin to Jim Jaspers - the cosmic-entities had played along with his schemes in order to observe him and nurture the power he had in the hopes he would learn to control them, this new origin is controversial however and may or may not be fact (although as it stands the official statement by Marvel is that the Beyonder is a rogue Cosmic Cube).