Ah, thanks for the explanation! It seems the title of the chapter "まごころを、シカに" parodies the Japanese title of the movie "The End of Evangelion" ("まごころを、君に"), so that makes a lot of sense now.The underground GeoFront was referencing the underground GeoFront base in Evangelion. The screens with the warning signs are also a reference to Evangelion's.
When Go-Daigo failed in his first attempt to overthrow the bakufu a few years before (Shochu incident), they didn't take any direct action against him either. Well, they did exile (and torture) some of his associates both times, but still, very patient.They waited for 4 whole year before acting? The bakufu at that time must be a very patient group huh.