The problem with this question is that most people that ask it don't understand the question they are asking. Equations such as "E=mc^2" on their own explain nothing because they sweep an enormous amount of very complicated details under the rug. For a meaningful discussion of things like "Where did the energy come from?", one has to be able to understand the very hairy internal mathematics of the equations that most people assume to be true. In fact, most people's common understanding of the meaning of these equations isn't actually correct; in reality they are far more complicated and have strange side-effects, but the "made for TV" explanations are easier to digest for most people. One of the weird consequences of the "cool physics for the masses" books that have become popular is that there is a huge crowd of people that THINK they understand physics who really don't. It is analogous to armchair warriors who think watching action movies gives them all the knowledge of a Special Forces operator.