...Most of the main plot.
I’m sort of kidding, but sort of not; from what I recall, BE had a lot of sub-adversaries and red herring bosses, or side-stories that could at time she genuinely interesting, and were only connected to the story because Owlman and Cluemaster called them in as distractions and opportunistic allies. That was part of the reason BE’s overarching plot kind of failed - Owlman’s arrival was a last minute thing, and once they started bringing everything together, a lot of the plotlines got kind fo dumb.
In contrast, B&RE established Mother as the villain early on, and was mostly a year long investigation and hunting down of Mother... which didn’t quite work, as Mother was kind of bland.