Beyonder is a bunch of energy that turned into a person. Confused? Let me explain. A group known as the Beyonders, which just mean people who are so beyond what we think of as people that it's best just to call them Beyonders, put these Cubes of energy out into existence. The purpose of the Cubes was to alter energy. I guess that's the sort of thing Beyonders do. After Molecule Man took the last Cube, the leftover energy became the Beyonder.
The Beyonder checked out Earth for a while, then got bored so he faked his own death. Kind of irrational to me, but people do what they do. Eventually the other Cubes told The Beyond what he is, "my man, you're just a cube." That's when Molecule Man found him and was like, "Dude, should we merge completely?" so they did and became a Cosmic Cube again.