The thing about this games is that because we don´t know a lot about the motivations of,... anyone really, they all come across as incredibly shady. What we know of Ella´s backstory and what she does in game with the pills, Jake and Derek makes it clear that she isn´t an heroic character, but the part with the orphans, her friendliness with the MC and the fact that we don´t know a lot about her foes makes it hard to discern is she´s full on villanous or just a well intentioned extremist.
H.E.R.O is backed by a world goverment which is implied to be somewhat dystopian, their main researcher makes deals with the mob for test subjects and they have been covering up monster attacks for years, but then again, we don´t know if their doing out of pragmatism or for some other sinister goal.
And then there´s the monsters themselves, but we don´t know enough about them to speculate shit about their motives.
The ones in this game that we can call outright evil are the Aldains, the NTR dude in Liz route and Amber´s Mother.