The defense against the Black Swarm wishing to rob Cimexus of its freedom. The resistance is scattered across smaller groups, like the Guardians who protect the Origins, and the many small villages who sent out the drones who are most of the Black Swarm's lesser ranks, all but of course Dr. Gidoh and at least three of the Four Generals, and the five characters who believed in the drones enough to not submit- the new leaders of the resistance, Dr. Sakuma and Yamato, and Tsubasa, Yui, K-Buto, and Shoya.
As the game moves forward, the Black Swarm's power becomes increasingly apparent in that, canonically, in the entire last two thirds of the game, it is canonical that they are simply running through the battlefields trying not to be destroyed. It should be noted, however sadly, that it is absolutely impossible to win the final mission without fighting in the Badlands, which canonically comes after the Story Mode, meaning that outside of the game, the resistance would fail without fail.
The emblem of the resistance is entirely based on a rhinoceros beetle, and includes wings, hinting at at least a butterfly, but scarabs do have wings too. No visual mention of a snail, firefly, or stag beetle is present on the emblem. Their color is red, again for Yamato, and the unthinking and stubborn heroic red most anime bases their hero on. The rhinoceros beetle and red are actually very accurate to their cause, as the resistance canonically has a very difficult, and almost impossible, time fighting for justice and good. The rhinoceros beetle is the one drone that is intended to purposely soak up hits and deal heavy damage back, being the center of the battle and risking himself greatly every turn, in order to flip the odds back in the group's favor.
It is questionable whether the resistance truly deserves to be called the 'good guys' if the game's lighthearted kid-friendly abandon to the citizens of Cimexus is taken into serious consideration. At one point, Tsubasa legitimately believes that Dor-O's food synthesisers would cannibalize the very intelligent and living citizens of Cimexus and is revulsed because bugs would taste gross. At a certain twist which devastates Cimexus-kind, the optional Talk dialogue that chapter is entirely about the resistance's leader, Yamato, being upset that his friend has stayed gone for so far half the game's length, and all of the human resistance members being worried about him. During the endgame, Yamato's personality bends highly noticably to fit the plot, and forgives all but one of the true villains who ravaged Cimexus and killed hundreds of innocents, with open arms. Dr. Sakuma even screams out that he will forgive Dr. Gidoh if he just stops then, in the final chapter, after everything he'd done. Perhaps the most disturbing part is that, no matter what the humans of the resistance choose to do, the Cimexans are powerless to them, and will unquestionably support them, especially peaceful decisions like sparing Dr. Gidoh.
The guard on the bottom of the emblem is supposed to appear as a defensive symbol, but it can also be taken as the shoulders/neck of a very evil armored face, with its wings as feathered horns, and a knightly armored assassin mask over its face. The eyes are the base of the wings, and is actually ironically cemented by the pixel disparity in the lines appearing as small irises. In Japan, such an appearance might look heroic, espcially with the beetle horn on the forehead, but that aspect is lost on the Western audience, and together with the eyes, make it difficult not to see evil when the viewer notices that the emblem is dually a face.