What two elements make up over 99% of the observable universe?
Hydrogen and helium.
Mostly, these are the elements formed in the Big Ban,and they have been with us. Heavier elements, of course, are produced in stars by fusion, and also by even more violent events such as supernovae, but even 14 billion years after the Big Bang these processes have impacted only a small part of all the matter in the Universe.
Also see here.