my interpretation is that the alien killing the scientists is one of the participants who went through the journey of escaping back into a physical form. but instead of gaining a human body you became an alien creature. and maybe the blue suit guy works for the same org as the scientists in the facility that the alien escapes from.
maybe the eyeball creatures are these same escaped creatures who now possess cursed knowledge as a result of their experience in the other world that they escaped from. so in the second half the perspective switches to people who are either fighting against the creatures or seeking their knowledge.
that's just my theory. also not sure how the last game fits in exactly