My fan fiction is originally they were humans that had bio-engineered themselves into super-beings and dominated the galaxy thereafter. However, others rebelled against them and imprisoned them on Krypton. A virus introduced to their genes shut off most of their powers under red spectrum radiation and the intense gravity of Krypton countered their powers of flight and super-strength. The original Kryptonians could not escape the prison planet. And an ultimate fail-safe was built into the core of the planet that would turn it into Kryptonite and kill them.