Boy, in the last 20 minutes the plot anvils starting falling out of the sky like frogs in a Biblical plague. In addition to what others have discussed, bad cops went on a rampage and brutally killed innocent people, only to be taken out by their fellow officers. The writers may have thought this was icing on the cake to make the final biting commentary on society, but I think it trivialized the whole issue of police brutality.
But even within the confines of the storyline, this new addition to the plot didn't make a lot of sense. So the Chemist roots out the bad cops by searching their disciplinary records, then gets (or forces?) them to take the black pill. Since they are not "talented" at what they do, they don't ascend to greatness, and instead become even worse cops, i.e., murderous pale people.
I know it's best not to dig too deeply into shows like this that Stop Making Sense. Could it be that this whole story has been an exercise in self-parody? See, the writers know that slinging dreck on the wall and seeing what sticks is enough to sell a series or a franchise. And it's not necessary to take a black pill if your lack of talent is not an obstacle. So maybe this was a brilliant tour de force, but we the audience are not "talented" enough to realize it!