I think John Harrison is an Android. Maybe Section 31 created a bunch of Android Super Soldiers, realized they became uncontrollable and started deactivating them. John escaped and is back for revenge. That's why he has super human powers.
Of course, Kirk and Spock end up defeating him by confusing him with these great lines: "Logic is a little tweeting bird chirping in a meadow. Logic is a wreath of pretty flowers which smell bad."