The year is 1969. Equipped with the mighty power that is science, humanity has used it for arms proliferation to cause destruction, all the while pushing for economic growth to produce more. As if to take advantage of humanity's paradox, the unknown "Invaders" have appeared, and the Alien Exterminating Global Intercept System, known as AEGIS, is created in secrecy as a countermeasure. Led by the UN, they assemble "Gate Keepers," a group of soldiers with superpowers, as the last line of defense for the Earth. One day, an ordinary high school boy Shun Ukiya is discovered by AEGIS as having the superpowers of a Gate Keeper, and he becomes the captain of the Gate Keepers. When his ability to open Gate blossoms, the story of a new battle begins.