The Theory of unification is a unified theory of everything; one that unifies gravity to the strong and weak nuclear forces, and electro-magnetism. One such theory is string theory.
When Dr. Rodney McKay thought he was about to die after becoming infected with alien nanites in an Ancient viral lab in Atlantis, he said to tell everyone that he was close to having a theory of unification, but the papers were lost when he was saving children . (SGA: "Hot Zone")
When implementing a hyperdrive generator on a Puddle Jumper, Rodney said "This is unbelievably complex physics here, alright? I mean, it makes string theory look like non-linear dynamics," string theory being one such theory. (SGA: "Lifeline")