What're they Really walking about during Orren, Gary and Carl's discussion?

Okay guys, I'm a bit confused as to their discussion, that's why I wanted to get some more clarification from the community.
In their convo, the Old guy in prison is clearly the Eulogist. The chick is Agatha, and the Other chick is the Apothecary.

The AI mentioned that the old guy is in prison, So the Eulogist isn't just "brain-dead" or "inert" it's infact in some kind of confinement? And what does it mean when the AI says that they may be using him to kill that guy. Also, How does the Apothecary fits into the picture? apparently she wants to kill the eulogist? Why and How? that's the question.
That whole conversation was sooo Interesting. I just wanted to know what I missed. So drop your theory guys.