Spoilers- The identity crisis!
So, John plays it off like he had just found out that Bruce was Batman. I think we can safely assume he knew since season 1. What are your guys thoughts. Do you think he's always known? If so, how do you think he found out while in Arkham?
Also, why do you think he's so desperate to be Bruce's friend in particular? Just because he's Batman?
And now that we know John is aware, would you still tell Gordon? Or is that too many people?
How do you think things will be handled with Waller? She's proven to be somewhat of an enemy but still has the leverage of knowing Bruce and Batman are one and the same.
Would love to hear everyone's thoughts. 
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I think he suspected it in season 1 but only had it confirmed in season 2
I don't trust John one bit but I told him I did because I want to remain on his good side. He needs to go back to Arkham and get further therapy so if that's an option I'll take it.
As for Waller, I'm suspicious about what she's up to but I'm still very wary of Avesta. I just have a feeling she might not be as nice as she appears.
In agreement with everything you've said. I like Avesta and think she's cool, but I sense a back-stab to come our way in the future.
I've also noticed something subtle. Maybe I'm reading too much into this but when Avesta and Bruce are driving to the subway after the interference with her hearing aid, a message pops up on the screen in the car about something technological and when Bruce glances at it she quickly says "what was that Bruce? Did you say something?" Now, maybe it was just the hearing aid but the message looked like there was other tech at play.
Hmmm... I'll have to pay close attention to that when I get the chance to replay. I will say her expressions when Bruce isn't looking at her have me on edge. I mean, I'm hoping she turns out to be a legitimate good guy... but my gaming-gut says no.
I hope she turns out to be a good guy as well. I could even see her taking over the Agency if Waller goes down but there's just something about her.....
After playing episode 4 I'm starting to belive in the Talia Al Goul theory. Mainly because of what the lotus virus and riddler blood combined look to be
The Lazarus Pit
Just imagine if that was the case.
I swear in season one, in the asylum, John straight out tells Bruce that he knows he is Batman. That's why the scene in season 2 episode 4 confused me so much. Did I remember season 1 wrong?
Well what he says is 'I know who you really are' but he could be talking about a number of things since he was claiming that Bruce has a dark side to him. But, since episode 4 of season 2, I'd have to agree that he was talking about knowing he was Batman.
I don't think John knew Bruce was Batman in S1. I actually don't think everything clicked until he looked up and saw the Bat Symbol, then he decided to see what would happen if he tried to give the laptop to Batman. Then, Bruce either giving up himself or showing off his moves during the SANCTUS raid confirms his suspicion since he goes up to Bruce and says "Nice moves buddy..."
Yeah, I was kinda peeved I had to save Harley. I was all like 'perfect opportunity for her to die and it seem like an accident... dangit Bruce.' Then he not only saves her but basically outs himself to John. lol.