I finished the game yesterday and while I enjoyed playing it I also find th estory not that strong in some parts and I think some thing were not explained well or at all. Through the game you have to piece together things that characters should know because it is world they live in but the game half acts like you should know them too as it dumps them on player and half like it is what you are to discover even though characters shoudl be aware of them already. I more prefer when things you are discovering are unknown to characters and world is explained more to players.

What I would like know and those are things that even characters don't know, I suppose, is what was the blue goo corrupting things and who was the real He you fight at the very end?
Was it ever explained anywhere?

The game's story is a mess, or at least it's not well told.

The players made a wiki, and the story is much better explained in there. If you don't enjoy comic book style plot, made mostly of twists and betrayals and recurring villains etc I recommend just skipping all dialogue and cutscenes and reading about a character later if you care.

Heh, I it's been less than 3 years and I don't remember single beat of the story. No goo, no He, nothing. :-) I don't think story one has to hunt outside of a game, somewhere on the wiki, is not well written one.

I wonder what state I was in when I wrote that OP? I have trouble understanding it myself.

Thanks for the answer anyway.