Dr. Oliver Thredson getting various facial injuries (Getting a picture frame smashed onto his face, and later a fire extinguisher) signifies that he's starting to look more like his alter ego Bloody Face.
In "Murder House", Zachary Quinto's character attempts to please his boyfriend by buying and wearing a rubber bondage suit that later becomes the costume of the 'Rubber Man' murderer. Said boyfriend dismisses it, saying he prefers leather. In "Asylum", Quinto's character turns out to be the 'Bloody Face' murderer, whose mask is made from the leathery remains of women's skin.
Dr. Thredson is left alone with a demon-possessed boy early on in the series. The scene cuts away; when it returns, the boy is in convulsions, and the clinically-minded Doctor recommends sedating him. In a later episode it is revealed that the Demon possessing the boy was aware that Thredson is "Bloody Face". Therefore it is more-than-likely that Thredson panicked and killed the boy by lethal injection in order to protect his secret life.
Lana's alterations to her book make much more sense if she's still traumatized from other off-screen activities Thredson did to her, still coping with Wendy's death, and in a roundabout way, keeping her son from being sought out by people fascinated by Bloody Face. Even if she says her embellishments are largely because of ambition and societal norms at the time.
The song "Dominique" was composed and sung by Jeanine Deckers, a lesbian nun who killed herself. Rather fitting.
It gets worse. Deckers allegedly owed thousands in back taxes for song royalties. When she pleaded that she'd donated her royalties to her convent, the church refused to back her claim. Making her a lesbian nun who killed herself after being abandoned by the church.
The opening credits commonly don't include an actor appearing on the show until the episode they're actually appearing in. It may seem pretty odd, then, that Zachary Quinto is in the credits of the first episode despite Thredson not appearing in that episode at all. However, Bloody Face makes an appearance in that first episode. So from the beginning, the credits hinted at who Bloody Face really was.
Even better, look at the poster on the main trope page for the series. Bloody Face isn't just standing in the window behind Threadson. He's Threadson's shadow. The poster was showing us the truth all along.
Arden's disdain for Sister Jude finally makes sense since in it is revealed in Freak Show that he was responsible for amputating the legs of that season's Villain Protagonist Elsa (also played byJessica Lange) in a snuff film. Elsa managed to escape, so everytime Arden sees Sister Jude, he remembers his "experiment" that got away.
In relation to Arden's case above, Pepper being fond of Lana. She looks like two people she knew in the Freak Show after all.
It's not like she was responsible for what the devil did.
In a few short moments throughout the season when she regains control, she's shown to be horrified by what the demon did with her body. In the end, she regains enough control to help the Monseignor kill her with the demon still inside her.
Those creepy images you see in the opening theme of every episodes? The more violent ones are Thredson and Arden dissecting people.
So you think that Dominique song is annoying when listening to it on the show? Now imagine the inmates (who are not well) have to listen to it, All Day, EVERY day.
the season ends with the song playing to give the audience a feeling of going crazy (with everything horrible about to repeat all over again in an agitating loop).
In Madness Ends Lana's report shows that Briarcliff decayed after the nuns left. That's right, Briarcliff is worse off when managed by the State than when it was run by A Nazi war criminal, a serial killer and the Devil
Putting her son up for adoption was the kindest thing Lana could have done for him, as he would have never been able to be anything to the world other than "Bloody Face's son" if she had kept him. If she had been able to fight off the (understandable) need to see him, his life would most likely ended up much differently.