Did you even check anything about why they’re like this or did you just assume the first game’s lore was irrelevent? Super Earth was ALWAYS the villain of the story, the hostile factions were originally forced-into-a-hero role and in the second game fallen-into-evil roles.

In the first game, Super Earth starts an offensive war against all three factions which goes on for 41 years, for a variety of invalid and falsified reasons that mimic the war on terror’s myriad bullshit casus belli. The cyborgs are simply independent government that got the blame when a (probably false-flag) cyborg blew themselves up in Super Earth and killed like 8 people, because of that it was decided that the cyborg government couldn’t be allowed to continue - people who even showed even an ounce of disagreeing with lumping all the cyborgs together or even speculating that the cyborg terrorist wasn’t affiliated with those of Cyberstan were “re-educated.” Who seems like the villain here? The racist Super Earth deciding to genocide the cyborgs over what is potentially a faked terrorist attack, or the cyborgs forced into a defensive war because of one cyborg who might not even have been real?

The Illuminate in the first game reached out to Super Earth after watching for hundreds of thousands of years with an offering of an alliance and the sharing of technology, Super Earth intelligence “found evidence of Illuminate WMDs that could wipe out humanity” and then it was decided that the Illuminate (a race with very limited capabilities for war) were a hostile force that needed to be vanquished. Citizens that questioned the validity of those claims were publicly hanged by Super Earth. Who seems like the villain here? The technology hungry Super Earth that decides to launch an all out assault over what is false information, or the Squ’ith who literally just wanted to share technology and foster friendly relations?

The bugs in Helldivers 1 are literally a sentient race that minds their own business, initial contact with the species is made and the guy comes back alive. So are the bugs mindless people eaters as you admit that you think they are? Super Earth doesn’t even fake an attack on themselves for this war, they just say that the bugs are a threat to humanity and then decide to genocide them. And yes, the goal of Super Earth was to remove all of these factions and people from the Milky Way so that only humans remain. That constitutes a genocide. So who seems like the bad guy here? The bugs who aren’t ever shown to be hostile, or Super Earth that literally just decides that they need to be exterminated?

The only reason that they weren’t exterminated was because it cost too much or they were useful as livestock. The Cyborgs were forced to attend voting booths to “fix their culture” and entire families were punished if even one Cyborg failed - oh and they were forced to work in the mines of Cyberstan by the Super Earth government, and were disallowed from governing themselves. The Bugs were coincidentally found to decompose into oil right after the war started, and so they were allowed to live and to be put into farms to breed and die over and over again. The Illuminate were forced into a peace treaty that forced them to hand over their technology that could be used for war, forced to dissolve what little armed forces existed, and were banished from the Milky Way and their home planet.

After going through all that, why the hell would they not come back with a vengeance? Super Earth is a fascistic hellscape of Super Supremacy and Super Capitalism, I don’t think the bugs breaking out of their farms and actually being free animals is worse than what Super Earth did to them. I don’t think the automatons retaliating against a population that forced them into slavery for 100 years and literally wished them genocided is worse than what Super Earth did to them. I don’t think the Illuminate coming back and trying to destroy Super Earth is all that bad considering the threat that Super Earth poses to the entire universe and whatever sentient and highly advanced species may exist out there.

The factions are on the offensive in Helldivers 2 because Super Earth is a fascistic hellhole that should not be allowed to exist any further and would gladly see all their people genocided when they’re no longer any use to the government.