I think Ella already knowing us beforehand may not be that deep, she may just have seen us on the street and saw something inside the MC, thus she investigated him for a while, infiltrated his friend group the easiest way possible and made him eat the pill. Yeah, there's a posibility that she did other things to get close to us, sure. But i think she doesn't actually know everything there is to know about our MC, for example: I think his eyes being the way they are and the mistery of his mom's death are gonna play a big role later that Ella will not see coming.
Apart from that, I don't think we are gonna have to actually join one group or another, I think we will be freed from H.E.R.O someway and will go back to being a free agent, i don't see our MC as someone who likes being in an organization, he's too passive in his approach to things to the point where he'd rather just be by himself minding his bussines.
I mean, even if you are playing the hero route and always choosing the morally good choices he's still the type to watch the TV and see there's a monster roaming the street and be like "huh, interesting. Anyways, going to sleep" instead of trying to hunt that monster to save people (Or even to eat it and gain more power on a corruption path), until he runs into that monster one way or another.
