Gatekeepers 21 is set in 21st century, 32 years from the original Gatekeepers.
In these 32 years, Earth finally was set free from the invaders. Japan is prospered like never before. A.E.G.I.S still exists in smaller scale to investigate more on the invaders and the mechanics of the gate.
However, A.E.G.I.S network and Earth Defense Agency has detected enormous amount of Invaders infiltration in the human society. Under such circumstances, an elite Invader Hunters group is assembled with Ayane Isuzu and Miu Manduru as their first two members.