Mix Masters was a dimensional experiment that would recreate matter and create enemies for soldiersto fight in a very safe dimension. It was done to create the better man, and to also let the army test out their secret dimensional weapons, but it opened windows to all dimension, and the matter became self aware. Now the matter is leaking into the other dimensions, with it's only goal to test people(but it does this by trying to kill them), because that's what it was designed to do. Heroes from different universes fight to save their own kind together. 



Perhaps the final boss will be the most evolved program, while it has the ability to think and reason, it's still confined to it's code thinking "to test mankind". It thinks it's doing the right thing, and that if mankind fails they don't deserve to live. 